Burnt wires will cause misfires and generally make the engine run pretty crappy. Get those fixed and check the others before you get more involved in the diagnosis.
How many miles do you have on the trans? Shifting issues like that could be a few things like synchros, hydraulics, etc. Check the clutch fluid for debris or general cleanliness as a start.
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97 T/A Ram Air Convt
Forever dyno queen / 777rwhp 662 rwtq @ 17lbs / 10.2 @ 140
'24 Corvette Z06
'17 Sierra 2500HD Dmax
'17 Lex LS460
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