I just uploaded the 150 dpi Game Genie and TMNT 3 manuals, so it looks like problems 1, 2, and 4 are taken care of. I re-uploaded the Syphon Filter manual, but it doesn't seem to be adding to the directory.
Ah, I didn't see this post at first. Thanks, that's just the information I needed.
1. I'll check on the upload limit and server timeout. It may be set to something under 350MB but the timeout should be at least two hours. I see you were able to get the 95dpi version through eventually.
I resolved 2 and 3 here
4. I'm not sure why you got an error downloading that, everything seems to be in order. I'll see if I can recreate the problem. For some reason your Zelda manual ended up in the "Z" section so I'll get that moved over to the L's tonight.