If you got smoke only when you directly connected the ammeter leads together, then there is an excellent probability your ammeter WAS BURNT OUT TO START WITH! THIS will prevent current from passing through it, which will block most of the accessories under your dash. Read up on the "ammeter bypass." Check the resistance of that ammeter. I suspect its HIGH if not infinite by now.
REPLACE the fusible link. This can be done by purchasing generic fusible link wire of the proper size, which likely will be #14 AWG. Fusible link wires are customarily 2 AWG sizes smaller than the circuit they protect. To wit: if you have a #10 AWG wire, the fusible link will be 2 even sizes smaller; #14. Be sure and find what wires you smoked. Your short circuit will be connected to those. Of course, you may have just smoked the fusible link. They do that when they go, but it isn't too much.
Those ammeters are nothing BUT trouble! Get a voltmeter and attach it to the junction you make with the red ad black wires which formerly fed that ammeter.
One of those wires should have been fed by the fusible link, while the other should go pretty directly to the alternator. I feed my alternator directly to my battery, with a fusible link, then run my battery through the firewall to the junction of the ammeter wires. They act as parallel conductors thus from that feed, feeding everything! You add one additional fusible link, and eliminate a major electrical failure point by eliminating the ammeter.
I also upgrade my feed to #8 AWG, using #12 AWG fusible link wire, six inches. The two #10 wires formerly in series through the firestarter (ammeter) as I said, divide the current in approximate parallel fashion.
Whatever else is wrong with your wiring, this SHOULD help.