I hooked an 8.4 volt 3500 amp battery to my kraken and now it doesn't work
 

Hey, I thought the stock battery sucked (8.4 volt 1100 amp) so I bought two 8.4 volt 3500 amp batteries and a quick charger.
Anyhow the connections were different and the new battery had thicker wire so I bared both ends and twisted them up and taped them.
Anyhow the fuse blew right away so I removed it and hardwired it.
Now the gun doesn't work anymore.
Whats going on?

Maybe you wired it up in reverse?

The function of a fuse is to save your electronics from being damaged. It sounds like it did its job and initially stopped any damage from occuring. You then ignored this warning and ran a straight cable with no fuse. Now you have the glory of trying to figure out which electrical item you destroyed.

Nothings certain without looking, but it sounds to me like you either overheated and broke a wire somewhere or you toasted your motor, it could be wired in reverse, no harm in trying the other polarity at this point I think lol

so even though the voltages were the same the amperage difference could cause damage?

Not exactly... just how you have it wired. Shorting out, cooked motor, fryed trigger block, ect.

Well its starting to work but the batterys drain in about a minute.
Another thing is I continually have to push the trigger forward to reset it.

bad trigger spring?

Or the trigger contacts have melted if you removed the fuse and had the battery connected to the gun in reverse polarity. I've seen that happen before. This would explain the trigger becoming lodged in the fire position.

When you remove the fuse (the intentional weak point of any electrical system), you transfer that weak point to another component in the chain, be it motor, switch, selector or battery. One of them is going to give next.

Erm... wow. Sorry thats all i can think of...

Time for you to take it appart and test each part, start with the trigger assembly and the motor.

I bet 20bbs on a reverse wirering at start, then trigger contact melted.