Probably would indeed do the bare minimum. 3000 mile on a rebuild that long ago will be variable. If it was left sitting for several years and formed rust in cylinders, then it could possibly damage the rings/bores/pistons. Needs to come apart to really see what is what.
If 'twere me, I'd put some Marvel Mystery oil in the cylinders 5 and 6 and let it set a while and work it over by hand several times, and add a bit of MMOil each time, just on the off chance that the rings have gotten stuck in the grooves due to old crudded oil in the ring grooves. It may be a 'hail mary' with low odds to do any good, but you never know 'til you try. Stranger things have a happened inside engines. 'specially since cylinder 5 was obviously dead with the bad plug. And it would be worth seeing how it runs with #5 alive again.
Water out of the tailpipes while warming up is normal BTW. That is not any specific indication of problems.