kinda doesn't make sense... if you didnt attach the cable well enough, and the cable fell off the battery terminal, then that battery can not be shorted... because the cable is no longer connected to that battery.... The only battery that could be shorted in that scenario, is the one in whatever the vehicle was that you used to provide the boost with....
the only way the alternator would smoke is if you connected the battery backwards (positive to negative etc), or if you shorted the battery while the tractor was actually running - in which case your battery would probably crack and leak - and spill acid all over the place....
when you say "the electronics" started smoking - does that mean the ECU, dashboard, or what?.....
My suggestion is whatever was smoking, most probably requires replacement:
1. battery
2. alternator
3. ECU or whatever electronics you are referring to
4. wire harnesses
this does not sound like a quick fix... so if this repair job is too daunting, it may be time to call the dealer....
unfortunately when it comes to electronics, cooking it a little-bit is not equivalent to overheating an engine mechanically... an engine will cool down and still most likely be OK..... with electronics it doesnt work like that, once you see "smoke" - whatever part was smoking is "gone".... "toast"... "no-longer-works". It takes a fraction of a second to completely destroy electronic components....
cheers and good luck!
