Identifying a scroll is different from deciphering a scroll and neither requires expending the scroll.

Identifying
The detect magic spell determines if there're any magic auras in the area on the first round, the number of magic auras and the most potent aura in the area on the second, and where exactly those auras are and how powerful each is on the third. With a successful Knowledge (arcana) skill check (DC 15 + spell level), the caster can determine the aura's school of magic; this check apparently takes no time and is part of the 3rd-round detect magic effect. Doing this would tell the caster only the school of the spell or spells on the scroll.

A 3-round thorough examination of the object while employing the detect magic spell permits the caster to "[i]dentify the properties of a magic item" with a successful Spellcraft check (DC 15 + scroll's caster level). This tells the caster everything about the magic item, with apparently one exception. The caster knows whether the scroll is arcane or divine, what level spell is on it, what level the spell or spells are scribed at, and so on, but identifying doesn't reveal exactly what spell is on the scroll; to do that the caster must decipher the scroll.

These 3 rounds are in addition to the first 3 rounds leading to pinpointing each aura in the area of the spell detect magic. Events happen in order unless stated to happen simultaneously.

(The analyze dweomer spell also reveals these properties, but the word dweomer is difficult to say without laughing.)

Deciphering
To find out which spell is on the scroll (and subsequently be able to activate it) the caster must decipher the scroll, which requires a successful full-round Spellcraft skill check (DC 20 + spell level), a successful 1-minute Use Magic Device skill check (DC 25 + spell level), or the read magic spell.

After the scroll's deciphered, that scroll's always deciphered for that caster. No further checks need be made, and the scroll can be employed normally.

Don't conflate identifying with deciphering. The hairs are fine and difficult to split but the game splits them anyway: When a caster identifies an item's properties, he gets command words, number of charges, and so on (pretty much just like he read the item's description from the book) but not the name of the spell on the scroll; the caster gets that and the ability to activate the scroll from deciphering the scroll.

Note: That's weird and the Pathfinder Role-playing Game buries that on page 490: "The writing on a scroll must be deciphered before a character can... know exactly what spell it contains." This also isn't exclusive to Pathfinder--both the Dungeons and Dragons 3.0 and 3.5 Dungeon Master's Guides have the exact same language in their Deciphering a Scroll sections (pages 203 and 238, respectively).

Note: A solid but dangerous case can be made for skipping the identification step if the caster already knows what he's dealing with, much in the same way someone proficient with a sword can just whack fools with the sword instead of learning its maker, properties, and history before he starts using it. The DM rolls secretly to determine if a character deciphers gibberish via the Linguistics skill, but the player rolls openly to decipher a magic scroll via the Spellcraft skill or Use Magic Device skill, so right there the player will know it's a magic scroll and, if successful in deciphering it, know the spell on it. The character can then try to activate the scroll, but--and this is really a DM's call--the character still won't know any of the scroll's properties (such as it's spell level or the scriber's caster level) because the character's not identified the scroll's properties. Just as Fighter Joe can still take swings with a magic sword without knowing its exact properties, Wizard Jim can decipher a scroll and, if he meets the requirements, cast the spell from the scroll without knowing exactly what's going to happen. I've never seen a player want to do that, but I'd totally let him. That could be hilarious.

Other Tidbits: There are spells that straight-up answer questions and get information; one could possibly use those and make a big pile of information about a scroll. There are feats and classes that are scroll-specific, and those might be useful. I've ignored both because they seem to be beyond the question's scope.

You are mixing up Caster Level and Spell Level. The formula for pricing magic items is generally

CL × SL × X gp

where X varies depending on the type of item. The Spell Level is as listed in the spell’s description, and seems to be the number you are using for both Spell Level and Caster Level. However, Caster Level is different: it is a property you get for having levels in the class that grants the spell.

Caster Level in most classes is equal to your level in the class. Some (so-called “half-casters,” e.g. paladin and ranger) have Caster Level equal to only half their class level. There are even oddball cases that use a different scheme for determining Caster Level.

Furthermore, each class gains access to spells of a particular Spell Level only at a certain Caster Level, which is usually higher than the Spell Level itself. For example, clerics, druids, and wizards only get to cast 2nd-level spells at Caster Level 3, while bards, paladins, rangers, and sorcerers get them at Caster Level 4. This is the minimum Caster Level for those spells for those classes.

Items are usually crafted at minimum Caster Level to keep the cost down, but the Caster Level must be at least the Caster Level at which the Spell Level may first be cast. For a 2nd-level Druid spell like barkskin, that is Caster Level 3.

With all of this information, it becomes clear what’s going on. You should be multiplying Spell Level and Caster Level, i.e. 2×3, but you are multiplying Spell Level with itself, i.e. 2×2. If you use 2×3×(50 gp), you get the 300 gp you see in the other table.

For a 3rd-level Cleric spell like water walk, a cleric needs a minimum of Caster Level 5 to cast that, so the cost is 3×5×(50 gp), or exactly the 750 gp you see in the table.

While not usually done, you can craft things with higher Caster Level. For example, you could craft a water walk potion with Caster Level 10 (assuming you have a Caster Level of 10 or greater), so that it lasts longer and is harder to dispel. This would cost 3×10×(50 gp) = 1,500 gp. This gets prohibitively expensive quickly, so most people stick to minimum Caster Level most of the time.

Do note that when you create a magic item yourself, you only pay gold equal to half the item’s base value. Be careful about whether a given table is giving you the crafting cost or the base cost. Also, some spells require extra materials or XP to cast, which is also reflected in their cost to create, and therefore also in their base cost.

Anyway, as for DMing and charging players who want to buy items, base costs are usually equal to the market value of the item. Most of the time, I strongly recommend just leaving it at that; the pricing isn’t anything like perfect but it works well enough and changes can have very unexpected results. Costs can be tweaked to represent unusual economic situations (particularly high demand for a given item, perhaps), but generally speaking that sort of thing should be done very carefully, and I recommend new DMs avoid doing so until they have a pretty good grasp of how the economy and system works (or doesn’t).