I have wrecked out an old shower down to the wood subfloor, (2x8's), in preparation for the tile contractor to re-tile. The drain assembly (flange?), is a two piece cast iron affair threaded on to a metal drain pipe. I removed the top piece with the 3 bolts, but I'm stuck on how to remove the lower piece of the flange. I have attempted removal from above and under the house to no avail.

Do I need a special tool, or is trick to unscrewing the lower piece from the metal drain pipe?

The top part of the flange must be replaced due to rust damage to the drain cover threads. However, the lower piece seems to be usable. Can I simply replace the top and keep the lower part as is?

Scott, I'd wreck a bit more and cut out the drain back to an area where you would have room to install a PVC drain transition and new shower drain in the pan. Sometimes it just is not cost/time efficient to try to fix and old rusty chuck of junk.

Since the drain assembles are different I need to know if this is a custom tile shower with a shower pan or a all in one plastic base and enclosure.
Since it sounds like you have cast iron pipes I wouldn't tear everything apart and install a PVC drain. If you have a shower pan your drain should be looking like this,(see image) If If you're asking if you can just replace the top of the drain, the answer is yes you can. This is what I
D do since the bottom will be secured with a poured and caulked lead joint.
I'm just "winging it" here without knowing exactly what you have.
We'll discuss more when you answer me. Cheers, Tom