Electrical issues HAAALP!

[coeurdelovesyou]

So I've been using this page for some time now but have never actually made myself visible. I recently had a horrible horrible stupid moment where I was in a hurry and slapped my vans new battery in backwards due to the posts on the opposite side. I had a job I was late for and didn't wanna miss it.. I made matters worse. Now I'm 8 days deep trying to fix my troubles. First it blew out some fuses in the fuse box, as well as my fusible links except the 2.0 one which was still sparked to a crisp. I replaced everything including a new .5 fuse thanks to the fusible link thread on here. After these repairs I was able to get my car fired up(nothing wouldn't happen before,) as well as test some codes I'm reading which read 4, 6, and 11. My issue now is that I lack power when running, I haven't yet tested my alternator but I will tonight when I borrow my friends tester. I'l fire up the beast, sounds fine, battery is good, starter works like a charm, then I put the e brake down... dead. Start her back up, turn on the headlights.... dead. Start her back up, turn on the fan... dead. Occasionally the headlights will come on without killing the engine but its a rarity. I had my battery tested and its all good, I replaced the negative ground wire from battery to the engine block as it was before. I'm fresh out of ideas, I've read it could be poor ground connection? any Ideas are greatly appreciated, I promise I tried and tried to get her running before I turned for help but I'm growing desperate. Oh one more thing, all fuses replaced except the hazard/horn fuse in which it will burn any fuse I put in there, yesterday I tried to put a new fuse in and smoke started pouring from under my stereo? I went to un plug the fuse and it blew up in my hand(not dramatic.) Could this be caused by a short somewhere? I'm pretty amateur but I'm learning, throw anything at me I'll try and fix it. Cheers!