Vincent,
I'm a long way removed from working in that area but seem to recall not enough room to pull out of crankshaft. I think it may be possible to loosen the main bearing caps enough to get one out but would require some disassembly. Not that it helps now, but I've always attached the flywheel before finishing the engine and dropping it into the frame.
From my very limited experience - and more importantly having a bolt failure at that location (with lots of follow-on damage) - I really don't think attempting to re-thread is a good idea. The threads failed (possibly from over torque) so that material is already weak and may not be able to hold the needed torque.
The Service Manual indicates using a straight bolt and reaming out the tapered hole. Luckily for me, my dowels were reusable. Since I haven't done this alteration before, I'd try to replace those dowels - if possible.
The dowels show up in a search:
https://www.ebay.com/itm/Jeep-Willys-MB-GPW-CJ2A-Engine-Flywheel-Special-Dowel-Bolt-Set-G-503-/182918338630https://www.armyjeepparts.com/p-3717-dowel-bolt-crank-shaft-jeep-tapered-type-wo-632156.aspxhttp://www.classicjeepparts.com/en/engine/flywheel-to-crankshaft-dowel-conical-early.htmlOthers here have way more experience on this and will hopefully weigh in on their options.