Figured I go ahead and update this because of the lack of posts:
First off, it still doesn't rev over 2,000. So bummer there.
Took the crankshaft pulley off, timing covers, belt and front cam gear off. Replaced the front cam gear with the manual gear.
--The manual gear has different peaks on the gear for the sensor to read. They are more flat and wider, whereas the auto is almost pointed.
Tested the crankshaft position sensor under the timing covers, that reads fine. Put all the covers back on and put the motor back in time. (Fun process while in the car)
So as I was reading through a lot of swap posts and CL-S threads, I found out the J32a2 with the CL-S uses 2 crankshaft position sensors. One under the timing covers and one that reads the flywheel on the back of the transmission. Since I have the Accord transmission, I do not have this. But there is a threaded hole on the front of the Accord transmission that looks like this sensor would fit in there. So gonna try that out and see if anything works for this. The sensor may just need to read voltage, and it might throw it up into limp mode for a 5 grand rev limit. Or it might completely fix it. If that doesnt do anything, I'll try the sensor hole on the front of the trans and extend the wires and see if that works.
Worst case scenario and last result before either getting a standalone or Richie's harness, is to drill into the Accord trans where the CL-S sensor goes and see if that works. I've got detailed pictures of that, so that is a possibility. It goes into the bell housing, so no fluid loss.
So naturally you need to order the sensor. I tried every auto parts store in my area (AutoZone, NAPA, O'Reilly's, Advance, and a few others) and no had had it. Shocker there. All they had was the auto harness for under the timing covers. So I ordered one for OEMAcura. It's been 14 days and it still hasn't shipped. Called them and the sensor is currently being made in Japan, then being shipped over. So they estimated I should have it in a week to 10 days. I just want to drive the car. Just once before the salt goes on the roads.
Things I figured out during this adventure:
If using a J37 IM with the P2R adapter for the J32a2 throttle body, you have to use both of their thermal gaskets that they supply. It gives it just enough room for the throttle actuator to clear it while on the throttle. If you don't it grabs it and holds it, causing it to bounce idle around 2 grand. I had that issue while looking for vacuum leaks. Also there is a long bolt with a hex that comes with it, but is too long and will not seal properly (at least for me). Luckily, I had some extra intake manifold bolts (J32a3) laying around and one of them worked great.