jboldiga said:
I have over 800 resource files and about 60 source files.
Holy crap.

Ok, you've got me beat.
One thing actually that might help speed you up is to use folder references. For a long time I was adding each texture to the project as an individual resource, and yeah, it -did- get really slow. Then I discovered that I could just put all my textures in a folder, and then do the following:
Ctrl-Click the Resources Folder >> Add >> Existing Files...
Find the folder I want everything from (in my case, Textures), select it, click Add.
Select the "'Create Folder References' for any added folders" option, and click Add.
Then you have a blue folder icon instead of a yellow folder. What this does is it copies EVERYTHING in that folder to a same-named folder in your bundle root. You have to account for this when you're opening files (you can't use NSBundle pathForResource: anymore, you have to use a relative path from [NSBundle mainBundle] bundlePath), but it doesn't do depcalc on a per-file basis for those guys anymore.
A downside to this is that it seems to be even -more- flaky when determining what it needs to copy over, but since it was flaky already, I was already used to doing full rebuilds whenever I added a file, so I didn't mind that much.