Glad you got it working (well, from the sounds of it, sort of working anyway).
Hmm, what are the specs of the computer you're running this on? If it's as slow as you say, you may be running out of memory here. One thing you might want to try would be to REM out (add REM in front of the lines) 3 of the 5 zone servers booting up (leaving you with two running) in your Boot5zones.bat file. If you're just playing this solo, I don't see much need for running more than two (it's not like you can be in five places at once
). You may actually be able to get away with only one (I haven't tested this; two works fine for me), but I chose two just in case of some swapping needed.
You might also want to try some basic system optimization on your computer (clean up your hard disk, defrag, etc.) which may help some.
As far as the crashes to desktop are concerned, I can't say. Someone more knowledgable about the guts of the program itself may need to answer that. However, I can suggest that if you're not already using Telmet's EQEmu-0.4.4-DR1 binaries (as mentioned in my instructions you referred to), you should.