I can't remember what the machined mating surfaces at the inner C looks like on a ball joint Dana 60, it's been a while. If you could post up pics of the bad surfaces/holes, I can better help.
I'm pretty sure the upper uses a bushing with tapered ID (that the Ball Joint locks into) and the OD sides into a cylindrical bore in the inner C. The lower has a tapered hole, that locks in the tapered ball joint. If I remember right.
If one of the inner C's machined holes, the part that's factory welded to the axle housing tube, is buggered up, JB Weld epoxy isn't going to work... there's a LOT of load on those machined holes, you can't allow them to rattle loose and remain safe. These are precision fits with exacting tolerances. If this was a trail buggy and trailside repair, heck yeah, but a rig that does highway miles, I'd want no part in that.
Depending on how modified your current housing is, how much welding has been done compared to a factory Ford truck housing (Chris should be able to tell you that) if the housing is essentially 'stock Ford truck', you might locate a $400 craigslist, LKQ, or salvage yard housing and have your mechanic swap it out. In my area, those things are sought after, the rock crawler crowd upgrade to these, so they are in demand. Yours is likely 'year and barnd specific' meanning ny old Dana 60 ball joint housing isn't going to work. If the upfitter used a 1999-2004 Ford SD, you'll need to locate one of those.
Another alternative, is to pull the housing and have a machine shop weld up the buggered hole, re-machine it in a mill. I don't think 99.9% of the mechanics out there could pull off a quality weld and remachine the hole, on the vehicle. Personally I'm at home behind the handles of a Bridgeport and with precision machining, so if it were me, I'd do this one either myself, or farm it out to someone with the right set of skills, after having an in-depth conversation.
A third is to carefully cut off the bad inner C, grind off the welds wo/hurting the axle tube, and weld on a good one, an aftermaket one (not sure they exist for ball joint, but I know Reid offers new king pin versions, not interchangeable with ball joint) , maybe a used one harvested from another housing.
Here's an ebay link, but these have been flame cut off, and require clean up by a machinist cutting out the stub, boring out the ID, then prepping your old housing to a moderately precision fit, indexing it so the caster ends up correct, then welding. There's a lot of build threads on Pirate 4x4, youtube vids, that show guys removing their inner C, and reindexing it to restore caster on a truck w/huge lift, the process is about the same.