If you keep it really basic (carb, mechanical fuel pump or electrical with a pressure regulator, single wire HEI ignition or (gasp, horrors) an old school distributor with points, condensor, rotor and an external coil you can keep the "get it running" anxiety to a minimum - trying to blend together computerized harnesses is a real PAIN in the nethers (this I know from a "non-Jeep" project I dug myself into a few years back that started with "why CAN'T I put an Audi turbocharged engine into a VW rabbit?" - seemed simple at the outset (both owned by the same parent company - yeah - right) anyhow I found out and - after investing time and money had a "to hell with it" moment of clarity (and offloaded the "project" to some other poor sap - although - he was warned).
Even on (what should be) plug simple factory swaps (like putting a 350CI small block and a 4spd muncie into a '67 Chevy II that originally had 3 on the tree and an I6) problems can arise - you've just got to keep cool and work through 'em.
The less complex your engine management system is the easier the project will be - the issues of physically fitting everything in pale when compared to trying to diagnose why the crank trigger isn't firing or why the ECU just got fried ....
Keep grinning -
Steve