A couple of references you'll want:
For the alternator bracket replacement:
http://www.pbase.com/mainecruising/universal_alternator_bracket - the definitive source for the alternator bracket repair (the link should read /universal_alternator_bracket)
Also, maybe take a look at my blog of my experience doing the replacement:
http://www.ericsonyachts.org/infoexchange/entry.php?539-Alternator-Bracket-Replacement-Exhaust-Riser-Rebuild-and-More
For the gearcase repair/replacement:
http://realitycheck.me/docs/servicebulletins/sb_193 DC alternator mounting.pdf -- The original service bulletin from the mfg. Tells what parts you'll need to do a heliarc repair or a full gear case replacement. I don't know anything about JB Weld, but it seems I read of someone else who tried it. Don't know what their results were.
I had to do the alternator bracket mod after I bought my boat last year. Luckily, my gearcase survived until I changed things out this winter. All the writeups I read said that the gearcase is a part that is no longer available. While I believe this is true for the marine parts people, I did check with Kubota out of curiosity while I was looking for other parts. I was able to find a Kubota gearcase for $555 (part #19264-04020) that my local dealer said they could special order from Japan. The problem with Kubota parts is that there is no direct cross reference for part numbers between the marine engines and the tractor engines. You'd have to do your homework to make sure you got the right part (if it is still available). If so, it's a tough call..... it will be a lot of labor to pull the old gearcase whether you decide to repair or replace. Hard to know whether to roll the dice with a repair or spring for a new $500 part.
Too bad about your gearcase. Best of luck.
Ken