I am pretty sure that the rules never clarify beyond what you have already quoted, and I am certain that the rules you have quoted are not definitive on this point.

I, and literally everyone I have ever played with or talked to, have always assumed that casting spells with both material and somatic components takes one hand. Never really paid very much attention to it. But I suppose the assumption was either that the material component is consumed before the gesturing takes place, or else that the gesturing is done with the hand holding the material component.

Questions & Answers

• Question: Can everyday items function as foci and material components?
  Answer: Yes, unless the DM determines otherwise. The only reason I can think of for a DM to determine otherwise is if the DM says spell component pouches are themselves unique creations (e.g. they're connected to a plane of magic, they're specially prepared to prevent exhausting their contents), but I've never heard of this done in a game. Being able to go without a spell component pouch and instead rely on separate foci and material components is especially appropriate for a low-level sorcerer who might otherwise be able to cast all of his Spells Known with only a bag of chicharrón and a comfortable sweater.¹
• Q: Can magic items be used as foci and material components?
  A: Yes. For example, using a decanter of endless water (DMG 254) (9,000 gp; 2 lbs.) as the focus for the spell bless water [trans] (PH 205) renders the next pint of water that issues from the decanter holy water but leaves the remaining water unaffected. For example, after killing the marauding grig druid who made it, a reasonable DM should allow his cloak of resistance +1 (DMG 253) (1,000 gp; 1 lb.) to function as the "miniature cloak" material component necessary for casting the spell resistance [abjur] (PH 272). The latter is wouldn't be considered a wise use of resources, however.
• Q: Does a focus or material component that's the subject of an ongoing magical effect change the effect of a spell that employs that focus or expends that material component?
  A: No. As long as the focus or material components satisfy the DM's opinion of the focus or material components needed for the spell, the spell can be cast, but a spell only does what the spell says it does. It would be problematic and tedious to develop such house rules as they would have to cover a huge range of possibilities unless either options were restricted to a very small set of effects (e.g. while the "pair of small iron bars attached to two small canine statuettes, one black and one white" needed as the arcane focus for the 6th-level Sor/Wiz spell repulsion [trans] (271-2) are the subject of the 1st-level Sor/Wiz spell grease [conj] (237), in addition to the standard effects of the spell repulsion, creatures who fail the Will saving throw are rendered prone) or the DM just concocted effects on the fly, a tremendous risk that can have serious long-term consequences on the campaign.
• Q: Are there rules for changing a spell's effects using material components?
  A. Yes. There are evil spell components (BoVD 45-6), good spell components (BE 37-8), metamagic components (UA 139-51), optional material components (CM 135-6), and optional material components (ECS 91-2).
• Q: What would you suggest if a player attempts to cast a spell using an unusual but appropriate focus or unusual but appropriate material components, hoping for an unusual effect?
  A: I'd probably say The spell works as written. Dungeons and Dragons 3.5 is already a hilariously expansive game with many, many options, and another layer of options on the game's already optimal problem-solving strategy seems indulgent. That said, if all of my players were interested in the increased complexity, I'd consider letting them experiment with alternative material components for minor changes to a spell's effects, but I'd keep ones that were important to the plot or significantly powerful rare or secret, to be located or discovered as the campaign progressed.

Kelgore's Fire Bolt

The 1st-level Sor/Wiz spell Kelgore's fire bolt [conj/evoc] (PH2 116) specifically "conjures a small orb of rock and sheathes it in arcane energy." There's just no way to substitute a different orb of rock for the orb of rock that's conjured, in much the same way a javelin of lightning (DMG 226) (1,500 gp; 2 lbs.) can't be substituted for the "stroke of electrical energy" in the 3rd-level Sor/Wiz spell lightning bolt [evoc] (PH 248). The magic creates the effect.

However, house rules might have the "handful of ashes" that are the spell Kelgore's fire bolt's material component change the spell's effect if the ashes were, for example, from a golem manual (iron) (DMG 258) (35,000 gp; 5 lbs.) or an ingredient a wizard had planned to use to create a homunculus (MM 154).

To expand on the first question and its answer, here's

A Brief History of Focus and Material Components in Dungeons and Dragons from Advanced Dungeons and Dragons to Dungeons and Dragons 3.5

Being a caster in the earlier days of Dungeons and Dragons meant managing focus and material components. Although house rules often eliminated them, were they not eliminated they afforded the DM the opportunity to deny a caster his ability to cast some spells, forcing the caster to solve problems using different spells or even different means entirely (e.g. fleeing; grappling, overbearing, and pummeling; lateral thinking; role-playing; throwing daggers or darts).

Spoiler for an Over-30-year-old Adventure Module

That said, even the most famous old school railroading adventure module, Schick's A4: In the Dungeons of the Slave Lords (1980), before play begins, removes all PCs' possessions, not just magic-users' components and spellbooks. Don't worry! Magic-users and illusionists get some scrolls.

The Player's Handbook (1978) says that

Material components for spells are assumed to be kept in little pockets, stored in the folds and small pockets of the spell caster's garb. Of course, some material components are too bulky, and in these cases the materials must be accounted for carefully. Also, some materials are rare, and these must be found and acquired by the spell user. (40)

Thus, beyond explicitly being able to "add or delete entire spells" as he was given permission to do a mere paragraph earlier, the DM is further given tacit permission to restrict access to spells by making some obviously inexpensive material components rare (e.g. the "tiny ball composed of bat guano and sulphur" [sic] as the material component for the 3rd-level magic-user spell fireball (73); the "small magnetized iron bars attached to two small canine statuettes, one ivory and one ebony" as the material component for the 6th-level magic-user spell repulsion (86)). Material components were both bad jokes and campaign management mechanisms.

In the Player's Handbook (1989, 1996) material components are handled differently:

When material components are required, these are listed in the spell description. Spell components are expended as the spell is cast, unless otherwise noted. [...] For cases in which material components are expended at the end of the spell [...] premature destruction of the components ends the spell. (114)

And that's it. Without optional rules material components are flavor text. A caster has the material components with which to cast his spells unless the DM uses the the section titled Spell Components (Optional Rules):

If the spell components optional rule is used in your campaign, your wizard or priest must have these items to cast the spell. Without them, he is helpless, even if the spell is memorized. For simplicity of play, it is best to assume that any spellcaster with any sense has a supply of common items he is likely to need--wax, feathers, paint, sand, sticks, and fluff, for example. For expensive and rare items, it is perfectly proper for your DM to insist that special effort be made to obtain these items. After all, you simply can't assume your character has a valuable pearl handy whenever he needs one! (113)

But the inclusion of the spell component pouch (5 gp; 3 lbs.) (PH 108, 111) in the Player's Handbook (2000) removed (except via rule O) the DM's ability to control what he considered problematic spells via making obviously inexpensive foci and components rare. Every wizard with a spell component pouch has within a "tiny ball of bat guano and sulfur" to cast the spell fireball (203-4) and a "pair of small iron bars attached to two small canine statuettes, one black and one white" to cast the spell repulsion (245)² in addition to nigh infinite edible live spiders, miniature cloaks, powdered herring scales, undead creature bones, will-o'-wisp essence, and other gooey, icky, stinky stuff that must make anyone who carries a spell component pouch smell like a grease fire in crap factory.

War Story
The 1st-level magic-user spell identify (Player's Handbook (1978) 66-7) not only reduces the caster's Constitution score by 8 (knocking him unconscious for 24 hours if his score's reduced below 3) and only provides vague indications of what the magic item does if the caster first succeeds on d% (15% +5% per caster level) then successfully makes a saving throw versus magic, but also the spell identify has as its material components

• a 100 gp pearl,
• an owl feather,
• wine, and
• a live miniature carp.

Making sure goldfish survive while exploring a dungeon is difficult but necessary, as when a new magic item is found the "item to be identified must be examined by the magic-user within 1 hour per level of experience of the examiner after it has been discovered, or all readable impressions will have been blended into those of the characters who have possessed it since."

The 1st-level wizard spell identify (Player's Handbook (1989, 1996) 175) changed many of spell's details, but perhaps the most important change for anyone who labored under a DM who didn't house rule away material components was that the new edition removed from the list of identify's material components the live miniature carp.

Also of Interest

• What is the point of a spell component pouch?
• How to make spell components relevant again?

¹ The material component for the spell grease [conj] (PH 237) is a "bit of pork rind or butter," and the material component for the spell silent image et. al. [illus] (PH 279) is a "bit of fleece."
² "...the whole array worth 50 gp" was added in the 2003 Player's Handbook 3.5 (272).