Just thought I'd provide some more feedback now I've had time to get some more play in.
Generally, I personally find it a big improvement, both in terms of reducing percieved (if not actual) metagaming and in making my clerics contribute more consistently over time. It is mostly a boost to my party in general adventuring rather than for main fights, and in a way that feels appropriate (and increases my affection for divine casters/fits with my RP vision thereof). Its also an excellent de facto convenience tweak, one I much prefer to vanilla buffing (either manual or with AI).
However, I think a couple of spells are long duration where they may have been better left as a combat protection rather than being given long duration.
Negative Plane Protection was clearly designed as a combat buff. Vampires really aren't very scary now- obviously, the standard tactic was send in two NPCs with the relevant items, but just like when dealing with beholders this is a still a change in game style and pacing that was worthwhile. Now, unless there is a mage vampires are totally worthless. At the least, a longer duration NPP would seem to warrant a substantially higher spell level, but I think a shorter (still increased but perhaps not to full encounter length) version is more desirable.
Similarly, Chaotic Commands is now very cheap making illithids go down to a non-issue- I can just massacre them, really. Obviously, I can basically do this anyway, but shorter durations make it tougher to clear out areas of them.
I agree with the principle of long duration buffs in general but where a spell is primarily used to render a type of enemy non-threatening I think its probably best left as a combat buff.
Shield of the Archons is similar; it already had a pretty good duration, and probably should be a cast per encounter buff- which makes sense given its nature. Long duration magic resistance is also a bit OP- its a very powerful effect which is rightly difficult to achieve in vanilla; even dispellable magic resistance is a bit too much at the cap of the spell.
Generally, I think the above spells would be better with a somewhat shorter duration in terms of balance- longer buffs should be reserved for less gamechanging effects.
Unrelated but I also think divine zeal is a little strong- I would go with +1 to hit, with +2 to hit, +1 to damage from level 11. Of course, thats optional so doesn't matter so much.
Of course, I expect the mod reflects your existing preferences for play which is fair enough, but never hurts to share I suppose/hope. Thanks for all the work.