I like the idea, but it's too rich.
You're basically saying a 1 HD creature is worth 75 gp equivalent value (as it's one to one to gp when used to make magic items), so it needs to give 75 gp less in cash money. Refer to the Pathfinder treasure value per encounter guidelines.
Let's compare against the example they use of an EL10 encounter with an 8 HD stone giant and 4 4 HD gargoyles. If you're using the medium pace that encounter should be worth 4250 gp. It looks like using your rules the PCs can soul-trap 4800 + 1200 + 1200 + 1200 + 1200 = 9600 septims, which is way high. I might discount it a little because of the need to cast the spell, but especially as the spell has no save I'd personally bring along a level 1 goon with a bunch of scrolls I've scribed for him to get the sweet, sweet free money. Even if they just trap the giant, that's more than the gp value that the encounter should provide - and that's with zero treasure over and above the soul.
Because face it, magic is the #1 use of money in games after a certain level - so I wouldn't discount it all that much.
What you need to do is match up "soul value" those charts in the PRD so you're not giving a huge windfall.
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.
Best Answer
Basically, those rules say that you have a 75% chance of being able to purchase any magic item whose value is lower than the Base Value of the settlement. In addition, the GM rolls up a number of Minor, Medium, and Major magic items as listed on the table, which are also available for purchase. These bonus items must all have a higher value than the settlement's base value.
I'll run through an example, to hopefully make this a little more clear.
Xylitol the Wizard enters the settlement of Sugarfree, a Large Town. He wishes to buy a number of magic items. Specifically, he wants to buy a Potion of Cure Light Wounds, a Headband of Vast Intelligence +2, and a scroll of Magic Missile.
The potion is worth 50 gp, and the scroll is worth 25 gp. Since the Base Value of the settlement is 2000 gp, both of these items are potentially available. Xylitol (or his GM) should make 2 percentile rolls, each with a 75% chance of success. If the first succeeds, then Xylitol can buy the potion. If the second succeeds, then he can buy the scroll. If either fail, then Xylitol cannot purchase the item at this settlement at this time.
The Headband is worth 4000 gp, which is above the settlement's base value. The only way that Xylitol will find this item here is if the GM rolls it up randomly.
At this point, the GM should use the Random Magic Item Generation to roll up 3d4 Minor, 2d4 Medium, and 1d4 Major magic items. If the GM rolls up any items that have a value under 2000 gp (the base value of the settlement), those items should be re-rolled until all of these items are worth more than 2000 gp.
The items that the GM rolled are now available for purchase immediately. If the Headband happened to be on the list of items rolled, then Xylitol can purchase it. Otherwise, he'll have to leave and find a different settlement to buy it at.