There is no auto HF, they were all 5-speeds. The "std" or "DX" was the only CRX offered with an auto-box.
IIRC, the CRX clutch disk changed diameter at some point during the 89 model year. I don't remember if it grew or shrank slightly, but I believe you can use the smaller disk with the flywheel that used the larger disk without issues, as long as you get the spline count right for the trans input shaft and clutch disk.
I had not heard that auto axles had smaller inboard ends. I have heard that the HF axles and CVs were smaller and less sturdy than the DX and Si versions, but I haven't verified that myself.
...I'd like to hear an update on this project as well! I'm now considering one of the lean-burn motors for my Si when the D16A6 finally gives up the ghost.
-soD