When special abilities modify the enhancement bonus, you use the total enhancement bonus to determine cost. This applies to weapons, armor and shields.
Special abilities count as additional bonuses for determining the market value of the item, but do not modify attack or damage bonuses (except where specifically noted). A single weapon cannot have a modified bonus (enhancement bonus plus special ability bonus equivalents) higher than +10.
Your example of a +1 Flaming weapon has a +2 enhancement bonus and thus costs 8000g + base item and masterworking.
Some qualities from outside of the SRD have direct cost modifiers like +300gp. These just add on to the price instead of changing the enhancement bonus.
Yes
Firstly, you can always upgrade items by paying the difference (DMG p288):
A creator can add new magical abilities to a magic item with no restrictions. The cost to do so is the same as if the item was not magical. Thus, a +1 longsword can be made into a +2 vorpal longsword, with the cost to create it being equal to that of a +2 vorpal sword minus the cost of a +1 sword.
Flame Tongue is slightly different because it has a unique ability, so that there technically is no +4 Flame Tongue in the books to upgrade to, but according to the FAQ (p.63), you can upgrade it if the DM gives permission:
That said, a DM willing to allow leeway in item creation could allow a character to upgrade such an item's capabilities, using the same guidelines as for improving any other item (see previous question).
Based on the examples given in the FAQ, Flame Tongue is a 20,715 gp +1 flaming burst longsword with a unique ability, and costs 2,400 gp more than a standard +1 flaming burst longsword.
You can therefore upgrade your weapon by paying the difference between a +1 flaming burst sword and the item you want to upgrade to.
As for level requirements, being level 12 and able to craft a weapon of up to +4, that means you can give the weapon an enhancement bonus of up to +4. That's actual enhancement bonus, so you can make a +4 weapon with as many special abilities as you like until you hit the hard limit of +10.
Creating a magic weapon has a special prerequisite: The creator’s caster level must be at least three times the enhancement bonus of the weapon. If an item has both an enhancement bonus and a special ability the higher of the two caster level requirements must be met.
This seems to imply that you also need to be level 12 to put a +4 equivalent special ability onto a weapon, though it doesn't specifically say this, so it's a little vague. It doesn't matter at all in your case since the only special ability higher than +4 is vorpal.
In your case, the +1 Flame Tongue is priced as +3 (Flaming Burst property is +2). This means if you upgrade it to +4 Flame Tongue, it is priced as a +6 weapon (plus the 2,400 gp for its special property). You can attach up to +4 in additional special abilities before you hit the +10 hard cap.
Best Answer
It's Caster Level 8
Your second interpretation is correct. Here's the rule itself:
Then from the Magic Weapons page:
From here, it's pretty clear that enhancement bonus and special abilities are distinct things. You combine them for the weapon cost (as the rule stats), but not for the crafting caster level requirement as each type has its own requirement. You just have to be able to meet all the requirements.
Thus, you need CL 6 (3x2) to make a +2 enhancement bonus, and CL 8 (and have access to the spells Chill Metal or Ice Storm) for Frost.
This also means all the weapons on the chart can be created without being epic level, as if you needed to be CL 9 to make your +2 Frost Weapon, it'd be impossible to do any combination that is >= +7 without epic levels. (You can't make a +7 sword without epic levels, but you can make a +5 Keen Frost one, which has the cost of a +7 equivalent weapon.)
It Could Be Caster Level 6
Depending on how you want to interpret the rules around prerequisites, you could create the weapon at CL 6 as a Druid (who get access to Chill Metal at level 3). The reason for that is these rule passages. From the SRD:
And from DMG p. 215:
Depending on how you read this, the prerequisite could only be access to the spell itself, rather than the CL listed. In that case a level 6 Druid could create the item (as they can do both +2 and have access to a required spell). A Sorceror would need to be level 8, as that's when they get access to Ice Storm.
I'm not 100% convinced this is how they intended it to work, but it makes an item entry like Universal Solvent make a lot more sense. It has a listed CL of 20, which for such a common an inexpensive item just seems really wonky if only the greatest spellcasters on the planet are able to create it (particularly since the required spell is available to Wizards at level 9).
If you use this interpretation, the CL listed on the item entries is a guideline, or what you'd expect a normal item of it's type to be if you find one in the world.