From Jerry Isner:
John,
Sounds to me like you have a good grasp on the basics. The bearings that are on each side of the differential where they fit into the case are smaller outside diameter on the HF than on the Si. If you want to use your HF case with the HF axles, yes, you can just use the Si countershaft and swap the Si ring gear onto the HF differential (ring gear bolts are left hand thread). Or conversely, you could swap the HF bearings onto the Si differential. Use the ZC input shaft with ZC gears on it and swap the HF 5th onto it. You need to use the ZC input shaft as 2nd gear is part of the shaft and is not removeable. (Luckily you don't have 21 spline 88 transmission or you would also need to change the clutch.) Swap the ZC 2 thru 4 gears onto the Si countershaft and the HF 5th. All of this would give you a ZC/Si hybrid.

If you want to use all ZC gears, just swap the ZC ring gear onto the HF differential (with the HF bearings to use the HF case or the ZC bearings to
use the ZC case), use both ZC main and counter shafts with ZC gears and swap on the HF 5th. There are lots of possibilities, depending on what parts you have and what you want to end up with. If you need more help, just let me know.
Jerry