Being frustrated is understandable, and grasping at straws after investing big bucks is too. That said, the previous advice for trouble-shooting is spot on.., so take it, or have a mechanic take it in order to go through the routine problem/solution checks advised.
I am confused. On your first post you said; "...overheating engine that was rebuilt (DUE to an overheat)". Your second post said; "...it's overheating that there's a correlation (esp. when it wasnt' beforehand??)".
My assumption is that a '99 engine was found, but had experienced an overheat issue, and thusly was rebuilt, and then installed. Correct?
This '99 engine was rebuilt, i.e., bearings, rings, etc., and then topped off with it's own original, possibly reworked head, correct?
Then this same engine that was rebuilt due to an overheating issue came to you, and due to further overheating you had a so-called 'new' head installed whereupon the overheating issue remains, correct?
Could you start over with your '99 engine history, i.e; when found, from before it was long ago hoisted above your XJ engine bay for installation, to a year ago when it suffered overheat conditions?
To be clearer;
Do you know the total approximate miles on the '99 engine before the installation into your '92 XJ, (as in; prior to the shop work done a year ago)?
Before the 2 grand shop work done a year ago, your engine was overheating, right? Did your XJ have any outward symptoms like loss of coolant waters, i.e., steam, fluid on the ground? Did you have water in oil, or oil in water?
You said the engine was rebuilt.., can you please explain exactly what was done according to your shop receipt? If you have lost it, try to obtain a copy from the shop, and report back please.
You said there was a "NEW" head installation to this shop rebuilt engine. Was it truly OEM new, or a reworked replacement?
Again I admit that I am confused by your write-up, but the advice others have given you so far are spot-on. I've only written this up for the sake of clarity that I, (and perhaps others), can be able to get involved to help you further.
I have had, and have seen engine blocks where there were leftover manufactures debris, and consequential crap plugging up various engine oil, and coolant passageways requiring removal of said, i.e., extractions, including pressurized air, and forced fluid checks to the engine carcass on the engine stand well before beginning restoration, i.e., line bore of the case for a crank, balancing crank check, cylinder restoration, proper new replacement parts, i.e., proper sized rings to new pistons, wrist pins, crank rods, bearings, etc., proper fit to head to case. Such a job is usually way higher than the 2 grand shop charge you mentioned leading me to believe you got a wham bam thank you for a partially quick engine rebuild.
member actually! it was from an automatic... i just popped a new thrust bearing in at the input shaft connection and it was more or less good to go. but it worked great for maybe five years.. no overheating or power isses of any kind. then i had a cooling system problem (blocked rad iirc) and had to get it 'rebuilt' including the rebore apparently due to heat damage in the head. 
