Hi, Wayman, great to hear your plans...I'm not sure what machining and parts cost in your neighborhood, but let me emphasize this: It will cost almost the same to rebuild a Jeep 4.0L into a 4.6L stroker as it will to rebuild a stock 4.0L inline six thoroughly.
That said, the added cost, at bare bones budget, will be the pistons and 258 crankshaft core or casting. You need the right pistons for the stroker, or you will not achieve proper piston height in the cylinders. On the piston side, if you use a hypereutectic type at 8.7:1 static compression with a zero-deck, the cost difference will be minimal. It will include block decking as part of the machining process to meet piston/deck height match. In my Hewes Performance video interviews, you will hear Tony Hewes talk about the rod and crankshaft matches and which pistons the different approaches require: http://www.4wdmechan...oker-Motor.html.
On a very low budget, conceivably, you could get by with a 258 crankshaft (serpentine belt short snout version is easier and popular, saves cost here) and connecting rods, bearings, a timing chain set with sprockets, a new camshaft and lifters, pistons/pins and rings, valves and valve springs with retainers and keepers, a complete overhaul gasket set (Felpro simplifies here), and a new oil pump and screen (Melling high volume). Hot tanking is a must, and this means new camshaft bearings, too. Freeze plugs, a water pump and oil filter round this out. This is a minimal parts list.
The minimal machining list after the hot tanking and camshaft bearing installation would be the cylinder head valve seat grinding, head decking, valve guide work (silicone bronze liners, minimally), block decking as needed for the stroker pistons, connecting rod and crankshaft reconditioning (as required) and piston fitting. Boring and honing the cylinders and line boring the crankshaft centerline is typical fare for a quality rebuild. Balancing reciprocating parts, if affordable, is a desirable add-on to the rebuild.
You mention a new clutch, and you should also have the flywheel resurfaced (if acceptable for this flywheel's design and condition, provide me with details on the year and application flywheel, I'll comment back) or replace it with a new one. As a reciprocally moving part, the flywheel would be among the balancing pieces...A crankshaft pilot bearing is required, one that will work with your later transmission and the 258 crankshaft.
Price machining locally, shop online for best buys on rebuild kits and pistons, etc. Have your block and head casting assessed by a reputable machine shop before plunging. Do you have a quality 258 crankshaft core already? Make sure the crankshaft will turn and polish at 0.010" or 0.020" undersize on the rods and mains, optimally 0.010"/0.010". If in a real pinch, and with a rougher crank core, 0.030" undersize is not terrible for an engine that will see reasonable use and not be desert racing. Block wise, a 0.030" oversize is acceptable, 0.040" would be on the edge, and 0.060" oversize for a Jeep 4.0L is more than I would want for proper cooling.
Share your findings. I'll comment objectively, I've been rebuilding engines professionally for 45 years and know what costs are reasonable. I am happy to comment and encourage other members to jump in here with helpful suggestions and experiences with a low-dollar stroker motor rebuild!