This morning I installed my new oil cooler, explanation here:
I seem to have a leaking oil cooler. (heat exchanger)
... and put the coolant back in the engine... ran it for final leak checks then dropped the Quickjacks and backed it out of the garage. So far I have done a couple of short trips around the neighborhood to make sure everything important works and to check again for leaks.
The transmission is marginally better at going into first than it was before the fluid change and new transmission mounts. I will perhaps try adjusting the shifter cables.
The other problem is that the temperature gauge doesn't work. I remembered seeing this thread
Coolant temperature sensor connector 2000 to 2002
... it seems to have the explanation. The replacement engine has a 2 pin temperature sensor and the original engine had a 4 pin connector... it seems the ECU is looking for the 4 pin signal like from the original engine. You can't just change the sensor because the wiring harness connector is 2 or 4 pin depending. The above thread has a workaround... till then I will drive with my computer on the passenger seat and check the temperature via my Durametric.
Three months for an engine swap is slow even for me, but it seems to be good. After some more road testing I will have to decide which Boxster to sell, this one which is an S or my 2000 base... which is running so well I am leaning towards keeping it. But maybe the S will be able to win me over. Decisions, decisions.