First glance...
Have some thoughts on the EOM fixes. Generally, I really like them.
[size=+2]Duration[/size]:
I like the Duration, Permanent. However, I never did understand why there weren't other durations between what we already have. Such as:
Duration, Concentration (0 MP)
Duration, Short (1 MP) - 10 minutes
*Duration, ???? (2 MP) - 30 minutes
Duration, Medium (3 MP) - 1 hour
*Duration, ???? (4 MP) - 5 hours
*Duration, ???? (5 MP) - 10 hours
*Duration, ???? (6 MP) - 14 hours
*Duration, ???? (7 MP) - 18 hours
Duration, Long (8 MP) - 1 day
Obviously, all the ones with * are the ones I added in. It just makes sense to have those individual MPs in there. When you want something to last as long as it can, and you NEVER have enough MPs, it's extremely useful to have options for each MP instead of going from 1 to 3 to 8. Just my $0.02 there. (Oh, I think Contingency should work the same way.)
[size=+2]Transform:[/size]
Cosmetic changes - Creatures: Like the addition.
Cosmetic changes - Objects: Like this also. But, does this mean that I can use TransForm Nature with 1 for area and make a blade of grass 10' in size? Or a toothpick into a 10' long plank? (Ooooo... I see the ole' pebble-into-bolder trick coming on...) Don't know if there should be some sort of limit besides "but you cannot increase their size to larger than the spell’s area of effect." Or, maybe it's just my evil, devious mind. ::wry smile::
Size changes:
First of all, using the tables provided, it looks like you would get NO penalties for going smaller. I think I'm seeing a copy/paste error.

I would guess that the strength and reach penalties should be highest at Fine and work it's way down. Should be opposite of increase size.
Secondly, it seems strange to have to spend 8 MPs to go from Gargantuan to Colossal, but only 4 to go from Medium to Large. (Or, for that matter, if you want to be silly about it, it takes 3 MPs to go from Medium to Medium.) Could you have something like a progressive system something like:
Size increases:
+2 MPs for each size category
+1 Str for each size category
+5 ft. reach for every 2 size categories beyond medium
Don't know if it would work with everything else in the system. I recognize that it's not as easy to figure everything, either. Just a different point of view.
Additionally, I have to say that I really like how you did the "greater of the two costs" for size change and transforming into a strong creature. Kudos. Makes a lot of sense.
(Believe me, I understand what you're going through trying to balance Transform. I had similar issues when I was trying to build my own system that I've mentioned before. And that was before CR's existed.)
[size=+2]Translate:[/size]
Have to agree that this should be it's own thing. I like it.
All in all, very good changes. Now, if I can just figure out how to get these changes into the PDF without buying Adobe Acrobat... ::wry smile::
Michael