If you can't reduce the number of files to less than 1000, you'll have to do without the web version and leave the game only in download mode, where you don't have that problem.
Viewing post in File Limit for Project ZIP
That's a shame, since the game isn't actually that big (around 150MB). I think the problem isn't so much joining all the sprites into single spreadsheets, since my game doesn't have that many sprites. The problem is that RPG Maker checks and requires default image and audio assets even if they're not used.