More electrical woes!

["Joseph M. Shaw, II" <MikeIIDC@domain.elided>]

Well, after a couple of successful endeavors into mechanics, I am right
back where you guys expect:  screwing things up marvelously!!!
I went and got a new alternator and mounted it.  Started the Scout with
no problem.  Guage was showing plenty of charge, lights were bright,
engine was running strongly.  I left it idling for a few minutes, as I
was going to check my idle speed and readjust my carb.  As I was playing
with the carb, I saw a small spark by the firewall, and looked up to see
a home repair with one of those screw-on connectors glowing and
smoking.  I immediately ran around the truck and turned it off, and came
back to see that the connector had melted.  I removed it, re-twisted the
wires, and black taped them for now to continue with my work.  I went to
try to start the Scout and got a dragging turnover, then nothing.  I
took my spare battery and hooked the jumper cables, same thing.  I took
off the cables, made sure they were clean, and reconnected.  Same
dragging turnover for about one "turn" and then dead.  I went to hook
the other battery up via jumper cable again, and got a HUGE spark when
trying to connect the last clamp.  I pulled it away, checked to see that
I was indeed hooking positive to positive and negative to negative.  I
had it right, so I tried again.  Another HUGE spark-much much more
violent than should be.  Once the clamps were on, nothing, but getting
them near each other and initial contact caused a huge spark.  I didn't
know what could cause this, but thought maybe I should just re-charge
the battery that was in there.  Upon connecting the charger, I got the
same reaction.  I checked my poles again, reconnected, and it sparked
big time again.  I got them on and the charger was alternating very
quickly and sparking itself-I could see the flash through the vents in
the charger.  It would click on very briefly, then click off and sit for
several seconds.  Each click was accompanied by a big spark.  I thought
that maybe something had drained the battery, but this reaction scared
me, so I disconnected the battery from the charger and decided I would
charge the other battery to try to start the engine with later.
What is going on?  Is it possible to do something to reverse the
polarity of the battery?  There is no way that the two wires I connected
were wrong, as they were still wrapped around each other when I took the
screw connecter off.  All I did was tighten up the connection.  I think
it was because they had some exposed wire showing before that they
connected with the firewall and shorted out or something.
So anyway, any of you electrical geniuses-Dan Nees, John Landry, et.
al., I am at your mercy.  Maybe I'll go out and throw the other battery
in and it will start right up and run happily ever after!  If anyone has
any ideas in the event that that does not happen, please let me know!

Thanks!

Michael