Well, while the Germans could have produced Stirling Engined U-Boats in WW2 (or immediately prior to it) the question is why would they have?

The Germans knew about the Snort from captured Dutch technical papers in 1940, but did not fit snorts until late 1943, the reason why? They did not need to.

The U-boats developed by Germany prior to WW2 were utterly conventional and similar to other nations types. No navy had given detailed thought to what the impact of radar would have on submarine warfare, mainly because prior to WW2 radars were not A. small enough to mount on aircraft, and B. Not powerfull enough to spot a surfaced U-Boat.
While shipborne radars were a significant threat to U-Boats, the loss suffered by U-Boats tells the story, once allied aircraft got powerfull airborne radars (coupled with effective ASW weapons) they killed U-Boats in huge numbers, much greater numbers than surface ships.

So the reason for fitting a snort (to escape airborne detection) only came about when the allies had radars capable of detecting surfaced U-Boats at significant ranges. As this did not happen until the introduction of 10cm radar, the U-Boats arm had no reason to hide under the
surface from aircraft.

To get back to your point about stirling engines, why would the U-Boat arm need them? They did not forsee the radar developments which would obsolete their craft, and their response was to design the Type XXI and Type XXIII, 'conventional' boats in that they still were diesel/electric powered. Exotic CC (closed Cylce) plants were experimented with, notably the Walter H202 powered drive system and the 'Kreislauf' Oxygen powered Diesel system, but none were used in frontline combat subs. Also, the Stirling system is only capable of relatively low power generation, its great for cruising at 3-5 knots in a barrier patrol, but pretty useles if you have to chase a convoy in the North Atlantic.

Basically my point is that the German Navy (like most large, hirearchical organisations) was only reactive to technological change, it rarely either A.Introduces radical new trechnology, or B. Forsees the introduction of new technology which will necessitate a change in its methods and behaviour.

Germany entered WW2 while it was attempting to build the Z-Plan, a plan for a 'balanced fleet' to match the Royal Navy. The plan contained BB's, BC's, CV's and about 250+ submarines (the plans was to run 1939-1948). All the designs were 'conventional' naval designs, it contained nothing radical or unusual (with the exception of large diesel powered destroyers). Thus the Kreigsmarine was utterly conventional and traditional, and the possibilty of a Stirling Engined U-Boat either prior to WW2 or during it would be pretty remote, to say the least.

Now i'm a great fan of 'what if' scenarios (Counter Factual History, to give it the correct name), but even the most outlandish CF history has to be grounded in facts. You cannot ignore the technological/political/economic/social background against which events take place. A more likely propulsion technology which the U-Boats might have used in WW2 would have been either the Walther drive of CC Diesels, and not Stirling engines.

Sniper.