Do you do your own mechanical work? If you do, I would suggest removing the engine and removing the heads to see what is up, and make your decision on what you find.
If you are paying someone to do all the work it would likely be less costly to just switch in a replacement engine.
On swapping a 3.2 for a 2.7... it is pretty straight forward if the new engine is a 2000 or 2001. If it is a 2001 there may be a problem with the temperature sensor which isn't complicated to work around. I know because I swapped a 2.7 for a 3.2 in my 2000S (temporarily) then installed a used 2001 3.2.
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Grant
Arctic Silver 2000 Boxster S - bought with a broken engine, back on the road with the engine replaced
Green 2000 Boxster 5-speed and 1978 928 auto
1987 924S 5-speed (Sold) - Blue 2000 Boxster 5 spd (Sold)
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