Well I finally committed to doing the procedure this weekend, and am happy to report that all 4 of my CPS2 shmups have been saved, and will live an additional 8-10 years on its fresh battery!
Because the battery is twice as long, and leads are exposed, I used an insulator to make sure it wouldn't hurt any other near by components. It doesn't look that pretty, but who can tell when its inside a case


Although it doesn't look like it in this crappy pic, these solder joiners are clean:

There was no problem fitting the board back into the case (plenty of headroom). There was also no need for a "helper" battery as some people suggested when you first remove the old battery. The CPS2shock website had all the details. In all it took about 30 minutes per board, from opening the case, desoldering, resoldering, and verifying clean connection and voltage, and re-assembling.