Well, I think i finally have the answers. I was getting errors in jEmplode, after awhile, on every synch would be a "checking media". Using hyper terminal, i would see errors like:
VM: do try to free pages failed for player
Memory allocation failed while retrying to read bitmaps, etc.
So....
I read Tony's FAQ (Yeah!).....
After testing continuity on the ide/motherboard connection i discovered a pin whose pad could actually be jiggled a little left and right. I was going to fix this! I went to Walmart got a Lenk 25 watt soldering iron and decided i was going to resolder every pin. As by recommendation, i got a toothpick and made sure each connection had plenty of flux on it. i held a magnifying glass that had a nice little round extra magnifier in one hand and the solder gun (with the smallest tip) in the other, i put a small bead of solder on the tip and put it on the pad for 2-3 seconds leaving behind a very nice bead. if the hand got shaky, i took a break. i ended up doing all pins except 3 right above a computer chip. these 3 solders luckily looked like some of the best before i went in and fixed the others right. i was very confident about what i had done and although slightly nervous, when the empeg was put back together, it booted and worked fine. I then did a couple of ~ 10 gig uploads with jEmplode on win2000se with no problems. right now, i'm about 1/3 through a 50 gig upload with no problems. Anyway, my point is jEmplode works fine, it was the user and hardware with the problem.

Two hints for jEmplode i think do work are:
1)if alot of zero refcounts which are put in root come up try to delete them all and synch. if jemplode comes back and says unable to synch "such and such artist/album" .... wait about 30 seconds or until your harddrive makes a noise and resynch - should continue deleting then.
2)adding lots of gigs at one time? delete soup playlists first.