Assuming you've never had the head replaced, if you're going to have the head and block ripped apart to remove any metal pices you might as well replace the head before it does grenade (known 0331 head casting issue) and get yourself a new valvetrain up top with a better head for strength and reliability.
After that you have choices - if you know that you've damaged the crank you probably have scored some of the bearings with metal pieces. It may be fine with out doing a bearing job too, but who knows?
You could probably get a JY engine for 500 bucks and just swap the whole powerplant, but then you need to deal with coil pack conversion to distributor or finding a 02-04 TJ motor which will get you the better head and coil pack ingnition. Newer motor bigger price.
Good luck, but you're probably into $500+ in repairs and some time with wrenches.
'00 XJ - Scampy the XJ
'10 Ram 1500 - Scampy's TB