1. no limit, except I suppose array size limit in 32bit ? 2GB of data size, but the Wii doesn't even have that much RAM. so, max size depends on the free memory left by the console. you can have more than 4000 games, it will just be very slow to load all of them at loader's launch.
2. your games are in wrong folder, wrong filename, or wrong format. Your loader has wrong settings, you forgot to list gamecube games.
3. that's right, probably the reason.
4. as you posted in the wrong thread for no reason, at least you could try the tool provided by this thread's developer ?
http://www.wiibackupmanager.co.uk/gcit.html, no idea if it renames the isos. there is also greywold gamecube tools (same, no idea what it really does), there's also DMToolBox, use raw option, don't convert or compress the iso.