If the alt is out in the open, I should not be a bid deal. The parts guy should know if it fits.
I have a different situation that is not stock. I actually had the rebuild shop "soup up" my existing alternator using the same housing. They had it up to 145 amps on the bench tester. It tested at 104 before they went to work on it.
I was not able to get over 12.5 volts with the original alternator and it was working perfect. (too many electrical gadgets added to the truck)
If they offer the larger alternator in a trailer package or HD package, it should fit.
The wire change is easy. You may have to add a 200 amp fuse if you end up eliminating the fuseable link. I used 4 ga, just because I had some laying around.
It sounded like your main problem was the altenator failed. If it's any hassle at all, I would just stay with the stock alternator for now, if you have not added any sound equipment or anything else that takes added power.
If you will be adding big sound gear in the future, you could get the alternator out of the way now.