Due to the scale length differences described by ImmortalSix, the only way to make a Strat-neck-Jag-body hybrid guitar play in tune would be to shift its bridge towards the lower bout.
Comparing Jaguar and Jazzmaster bridge positions will give you some idea.
Remember, Jaguar necks are 22 fret whereas Jazzmaster and vintage Stratocaster necks have only 21. Hence, the differences in the pocket and bridge post areas are not enormous.
If you really want to build an instrument like this, better to start with an unrouted Jaguar/Jazzmaster body blank. Try Allparts, Warmoth, WD Music et cetera.