Sounds like an interesting project you are planning there and would love to follow the build.
A while back there was a thread on Capri alternative engines being discussed with the Duratec V6 being mentioned which intrigued me also.
The S type Jag did have a manual option here in Aus. and uses the Getrag 221 transmission, It may still be easier sourcing a manual trans (even from the UK) than using an aftermarket ECU to run the S type auto. I could imagine splicing the Jaguar electronics into the Capri would be a complete nightmare with steering angle sensors etc. to be taken into the equation.
Will the S type's unusual front bowl sump clear the Capri cross member?
Is 240bhp enough for the effort? I would like to know what the above Duratec produces on aftermarket injection, it looks like a very tidy understated conversion.