ac and electrical confusion

I was trying to fix my AC on a 2001 intrepid es 3.2. I changed out the condenser and compressor. so we pulled the vacuum and started charging it. It quit taking freon after a can and a half plus the two oil cans but the clutch still hadn't kicked in. So we made a little jumper and checked the clutch off the battery terminals and it worked. I left it that way to finish charging the AC. So we thought we would run a temporary power to the fuse box. They hooked it to the line side of a fuse that ran off the key switch. When I turned the key on they saw a spark around the fuse box but didn't know where at around it more of a peripheral view. Then the car wouldn't even try to start. Everything comes up like it would but the dash lights just blink. We found a 40 amp green square fuse burned out and replaced it but it didn't change. So now I don't know where to start. Anyone have any ideas? Well I changed a fuse link that was shorted out I think but still didn't fix the problem. And now I'm stuck in second gear. Think its in the fuse box still but not sure. Any pointers?