Looks like you have a few things to look at but wanted to throw my 2 cents in here. My 1914 (basically the 982) was showing discharge on the ammeter as well and would kill batteries. I replaced a variety of parts before figuring out that my air gap was not properly set in my front PTO. I got that adjusted per the manual and the discharge issue went away. With your motor replacement this might not be the problem, but I didn't want to sit back if I could be of any help.
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Regards,
Adam
Proud owner of "Big Al" Cub Cadet 1914
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