To bring closure and hopefully help others searching this forum in the future, I will report my efforts to tune the carb pilot adjustments. I found a DMM (as John suggested) on closeout on eBay for $50 that could read rpm down to 2 rpm. I took the tupperware off and ran the bike without air filter assembly for this adjustment. I hooked my inductive pickup up the the cylinder I could get the best most stable reading on. For me, this was cylinder 1. Also recall, this is a California bike (different than the 49 states) that I put #40 pilot jets but left the 125 mains. I also had purchased the special honda tool. I was able to tell when the first cylinder dropped 50 rpm (#4, the hard one to get to). It was at 3/4 of a turn. I turned it out 7/8 per manual, to 1 5/8 turns, then rocked it a bit back and forth for best rpm. 1 5/8 turns was pretty much it. Recall that I had set them all to 1 7/8 initially. So the net change was turning it in 1/4 turn from where I have been riding the bike at. All the rest of the cylinders were pretty much the same. Cylinder 3 liked 1 1/2 turns the best. I then recynced the carbs. Put it back together and went for a ride. It seemed to run smoother, and burbled a lot less when letting off the throttle slowing down, then before. I will know more as I ride it this week. I expect to get better gas mileage. The top end seems unchanged.
I think I will leave it this way for now and ride it. If I ever need to get into the carbs again, I think I will follow Adam's advice and go to #128 main jets, drill the mufflers back out with a 3/8" drill, and retune the pilot screws again. From what I have seen, I think that would result in more power overall. The low end was definitely stronger, with no extra noise. Definitely would need the 128's to get the top end right.
While I had the tupperware off, I dug in and checked the valve clearances. This bike is at 34K. I had 3 intakes at .007" and 3 exhaust at .011", basically at the edge of spec. The rest were in the middle of allowable range. I am thinking I must have some crud on the valve seats to open the clearances a bit? Should be OK to run this way.
I also cleaned the shifting linkage and lubed it, and changed my oil to be a mix of shell rotella T4 (15-40 dino) and T6 (5-40 synthetic). It has been so hot here, I wanted to get some dino oil in there to see if it would help the bike to shift smoother. Seemed clunky, especially 1st to 2nd gear.
It did seem to help. Not dramatically, but some.
The last thing I want to do is figure out what to do for handlebar risers. I have a 1" extension on it now and I seem to get sore wrists even just riding around town. I am a bit nervous about going on a long ride. I am not sure if it will be painful. I am not sure I want to go so far as to put helibars on it. I am going on a 1200 mile round trip soon, so I need to figure it out.
Thank you all on this forum for helping me to get this bike in shape to ride!
James