Blowing fuses

Car was not used much, let battery run down, plus needed new one. Installed new battery, ran every once in awhile to keep battery charged and always ran radio, A/C, seats, mirrors, windows,
exterior lights ect. To make sure they worked, let battery run down and recharged it, started vehicle, ran fine, but A/C, windows, info/msg center, wipers and interior dome lights did not work.
Checked inside fuse panel and found the following fuse's blown, the following is taken from the owners guide. #25 a 7.5A Generic Electronic Module (GEM), Instrument Cluster, Securi-Lock,
#34 a 7.5A Rear Integrated Control Panel, CD and #36 a 7.5A EATC Memory, CD, Rear Integrated Control Panel, memory Seat, Message Center and a 10A fude in the Power Distribution
Box #5 Air Bag Diagnostic monitor. Replaced the fuses and they blew again, same three. Removed battery ground and replaced 10A, soon as I touched the ground wire to battery the 10A blew.
I pulled the GEM out and had read if the fuse didn't blow with it out then the GEM was bad (don't know about that, I am not a mechanic), anyways tried it, but the 10A blew again, that's the only fuse I tried. Have had a problem with the light/clock function on the radio, usually not lit, but every once in a while they come on, like there is a short there, never interfered with any thing else
working, and I have the Eddie Bauer, it has a removable 6 dicd cd player, that quit working quite a while ago, but cd player worked ok. Looking at the GEM, it looks OK to me, no rust or corrosion, is there a way to check it out to make sure its good. Only thing I ever did electrically to vehicle was disconnect the drivers side power window from the armrest control, the window came out of the track and try as I might I could not get it to stay in the track inside the door, everytime I got it back in, my wife would forget and I would have to pull the panels and get it back in, so I disconnected, still before recharging the battery, all worked fine. Any ideas on the cause and a cure. Some of the stuff I have read said to trace the wires out looking for frayed, cut ect.
Can't see how to do that when the majority of them are not visable. Don't really know what to do.