The con rod broke and went through the block and crankcase on my 2.5 manual last weekend.

Want to install a 4.0 but retain the manual gearbox from the original 2.5 The 4.0 is a 95 with auto transmission. How do I make this work with regard to the flywheel, flywheel sensor and ECU?

Im not sure that the ax5 that came with your 4 banger will work with the 4.o, i think you need an ax15..

going to go with the 4.0 auto transmission and swap the NP242 with the NP231 as it already has the SYE installed.

I think you're making a good choice. I have a PU with manual and my '96 XJ with auto, and am appreciating the auto more every time I drive it.