I'm going to post some things that worked for me. I was able to accomplish this in about an hour, mainly I think due to reading this thread and what people have done that worked or didn't. I saved a lot of time learning from you're guy's mistakes 
-My up/down ramp seemed loose, and it was. All three screws worked themselves loose, I didn't touch those prior.
-Stern sent me a new right wireform as balls were flying off the old one, works great now.
-I had balls going around the big side loop not being counted. two screws drops the opto bracket from the bottom and 2 plugs frees it. They looked straight enough, but they seemed to be pointing a bit up. I bend them both down, installed, and haven't missed a loop yet.
-Both my manual and auto launches were missing the loop. I adjusted the shooter rod, still missing. Based on advice here, I put a washer under the metal adjustment guide, didn't seem to help. My balls were hitting the bottom post.
Adjusting the guide as high as possible and 1 out of 4 were making the loop, 3 of 4 hitting the bottom post. Two things I did made all the difference. I had previously bent the prongs of the auto launcher so both sides were touching the ball, both at rest and at the end of it's action. What helped was bending both prongs inward toward the center so they contacted the ball closer to the center. Things were better, I was about 60%. What got me the rest of the way was tuning the coil power. Started at 255, went down to 250. Better. Went down to 240, same. Went to 245. Almost perfect. Went to 246, worse. Went to 244. At 244 I auto-plunged 10 in a row and all 10 made the loop. I pulled the plunger and with a full non-lazy plunge the ball made the loop 10 times in a row.
Put everything back together, and for the second time in the 100 games I've played I got the effect at the start of trooper multiball. Every ball for 3 games auto plunged correctly. I did have a couple misses on manual plunges, but I'm pretty sure the plunges were lazy.
As far as I'm concerned, it's fixed when it works for 100 games, but either way I am closer. I stopped playing so I can go to bed victorious 