I think you did a very good job overall.
Comprehend Languages [fix: gives a set bonus of +10 to Decipher Script skills instead of auto-deciphering]
My version let's you use Scry in place of Decipher Script together with a small additional bonus. However, that means keeping the 3.0 Scry skill in your game.
Divine Power [fix: remove the ability to cast spells while under the effect of Divine Power]
I don't consider the spell problimatic unless it is made Persistant.
Enlarge Person[fix: reduce duration to 1 rd/CL, and move to 3rd level]
I haven't had a particularly large problem with this spell in either the 3.0 or 3.5 version, but on the other hand, it is one of those spells that was made stronger in 3.5 without a whole lot of play testing. I find it hard to believe however that its a 3rd level spell - compare for example with Heroism or 3.5 Haste.
Entangle [fix: reduce radius to 10'; OR move to 3rd level]
The only problem with this spell is that the strength check it provokes is far too high. The spell is highly situational otherwise, and for example, I can't think of but one sitaution so far in my campaign where the spell could have been used because the combats have occurred in urban areas or underground for the most part. If you really have problems with this spells abuse, have it provide partial cover to those entangled by it and drop the strength/escape artist check to 15 or so and give a DC (25?) to break free as a free action.
And this is a clear case where if the spell is a problem, moving it to 3rd level does not help the situation under the RAW. That's because under RAW, it just makes the spell more powerful (Reflex save to avoid effect is now much harder).
Freedom of Movement [fix: move to 6th level]
I disagree. The main problem with this spell is it provides absolute immunity. Fix it to provide a bonus to reflex saves (and makes 1 not an automatic failure) and a bonus to escape artist checks that scales with caster level and its not only fine, you could concievably
reduce level.
Glitterdust [fix: "Spell Resistance: Yes (blinding only)"]
Not a big problem IMO. Better is, reduce duration of blinding to 1d4 rounds.
Knock [fix: adds a set +10 bonus to Open Lock checks]
Knock is indeed a problimatic spell, and I like your thinking here but you've nerfed the spell. Knock should provide an Open Lock bonus that scales with level (or allows you to use Scry in place of Open Lock if you retain 3.0 scry, which I do). Also, it should alternatively allow you to attempt to overcome a barriers break DC with a caster level check. Knock doesn't just open locks; it's can dislodge the bolt or bar on a barred door as well.
Mage's/Mordenkainen's Disjunction [fix: does not permanently destroy magic items, but does suppress them for CL rounds]
Only makes it more powerful. Of course, you may be aiming for something other than a power level fix with this.
Magic Circle vs. Evil/etc. [fix: see Protection from Evil, and move to 5th level]
Not a spell I have a problem with. My only fix would be to have the spell target an immobile point.
Mind Blank [fix: reduce duration to 10 min/CL]
No. My only problem with the spell is the absolute immunity. Change to provide a large bonus to Will saves vs. the appropriate spells and make it so that you don't automatically fail on a one.
Mirror Image [fix: move to 3rd level]
Doesn't really address the problem, if any. I don't have a problem with this spell as there are just too many counters from great cleave to fireball to dispel magic. To the extent that there is a problem, spell shouldn't stack with displacement/blur or other miss chance provoking spells at least to the extent that the images shouldn't gain a miss chance. I don't think it actually does reading the spell description, but it is apparently ambigious enough that some have interpreted it that way.
Planar Binding line [fix: don't set a HD cap, set a CR cap instead; or use Summon Monster-like tables for call-able creatures]
CR cap is appropriate though there are really only a handful of ways to break this spell. The fact that there is a chance of spell failure is a big balance on this spell.
Protection from Evil/etc. [fix: only protects from possession and mind control originating from creatures of the warded-against alignment, and move to 3rd level]
I don't have a problem with this spell. Duration is normally too short to have much of an effect. Spell is only problimatic if you use a niave version of Persistant Spell. Real solution is either don't use Persistant Spell or fix it so that the normal duration of the spell is taken into account when computing the new spell level.
Polymorph any Object [fix: there is no fix. This spell must go]
I don't have a problem with it. It's a high level spell. I'm not sure what you are seeing as the problem except possibly using this as a permenent polymorph self, which should be fixable in the way that the 1st edition versions of polymorph are fixable - mental state and personality is likely to shift with form.
Resist Energy [fix: do not increase the energy resistance at higher CLs]
I don't have a problem with this. High amounts of energy resistance are desirable at high level to allow flavorful environments to be traversed. Equally desirable is to have energy resistance penetration available to casters that depend heavily on a single element.
Shapechange [fix: remove the ability to use the spell-like and supernatural abilities of a creature you shapechange into, and introduce a clause stating that you cannot use any natural spellcasting the creature you shapechange into might have (such as a Planetar's Cleric spellcasting)]
Agreed.
Wall of Stone/Iron [fix: these spells need a duration other than instantaneous, I'm open to suggestions]
I don't have a real problem with these spells. If you are really worried, give them an XP cost.