I've never tried rapid rise, but until recently never had any issues getting set-ups, new and old, to index correctly. I usually put the bike on a work stand, have the barrel adjuster about 1/3 out, pull the cable taught with a pair of pliers and tighten the cable clamp. Sometimes, that's it, don't even need to fiddle with the barrel adjuster, other times just a quarter or half a turn and we're done.
Then I bought a used M737 rear derailleur. It was generally in pretty good shape, but the jockey wheels were very worn. I could get it to index shifting down, or up, but not in both directions. I then fitted a new set of BBB Rollerboys jockey wheels and bingo! Indexes perfectly in both directions.
So, it's definitely worth having a look at the jockey wheels if you're having indexing issues.