Take my advice with a grain of salt as I have a C6 but not a ZF5. However I have had manual vehicles before, and I have done several clutches.
Keep in mind your
1) Flywheel, clutch, pressure plate, and throwout bearing are a seperate system.
2) Your clutch pedal, master cylinder, and slave cylinder are a sperate system.
3) Your tranny is a seperate system.
4) Your drive shaft is a seperate system.
5) Your axle is a seperate system.
So try to isolate the issue, but remember it can be mutliple systems working together to cause the issue or a return of the issue. So look at all but I am guessing it is simply damage to the clutch system from the prior issues. (Once you have irregular wear on a clutch, replacement is generally the only way to fix it.)
You have shared
1) Your motor mounts may be compromised. You should think about replacing especially if the tranny is already coming loose. May be easier to do it with the tranny on, but you will be loosing the tranny mount and that may help.
2) You did not share, is your tranny cross member now replaced with a factory one or something you created/fabricated. (If fabricated, would suggest replacing with factory. Just take that out of the equation.)
3) You have a 2 year old LUK flywheel and hopefully a new LUK pressure plate and clutch went in at the same time. (Also did you clean the flywheel free of its protective coating?? If not that might be adding to your wows.)
4) That you have shifting issues twice. 1) Upon loosing your crossmember. 2) When your tranny cracked again.
5) Clutch works till it gets warm and starts to act up.
Other thoughts - (Could exasterbate your issues.)
1) How is the driveshaft? Good u-joints and good center support bearing?
2) How is your axle? Does it spin easily, do you have a lot of play in the pinnion and ring?
3) How is your clutch hydraulic system.
4) Does your engine move side to side when taking off in 1st/reverse gear. If your clutch is fighting the engine or tranny moving around, to your point this could ampliy the issue. However would guess it would happen cold or hot.
What I would do at this point -
1) I would confirm via inspection and lubricating that the clutch pedal, slave, and throwout bearing arm (If possible) all move gracefully and do not stick. It could be as simple as your clutch pedal, master, slave, or arm is causing the issue by not moving evenly/gracefully.
2) Check your axle and look for issues with the driveshaft. (Bad u-joints or center support bearing causing the tranny to wrestle with it.)
3) After confirming the above I would pull the tranny and -
a) Replace the clutch, pressure plate, and throwout bearing. It could be as simple as the clutch was bad and the springs or the center spline hole were not machined right. However its a good brand so sounds like these got damaged from the first two tranny issues. Now they likely have uneven wear, chadder markes, burn marks, or other damage from prior issues.
b) Resurface the flywheel. Always do this when replacing a clutch, its 50% of the clutch surface it uses. Always torque to spec and use blue locktight on the crankshaft/flywheel bolts.
c) Check to the new tranny you put in for input shaft for wear and the bearings for play. Other members if you have experience with a ZF5 please comment on how much play a input shaft should have. I do not know and would like to know.
d) Find out what if any lube you should put on the input shaft and clutch spline hole so it can slide smoothly. (This could cause some studder in releasing the clutch smoothly.)
e) Make sure your throwout bearing arm is lubed if needed and moves freely.
I know that sounds like a lot of work but again my thought is during your tranny issues, when the truck was not working as it should, it caused hot spots, or other anomolies to your clutch, pressure plate, and flywheel. Swapping trannies only fixed the bad housing and cause of the clutch failure, but did not fix the now compromised clutch.
Also check the other threads, I have not heard you have to pull the engine to do the motor mounts. But perhaps you are right, but confirm before you go to all that work.
FYI if you decide to light it on fire please do not use gasoline, the gassers will never let it down you have to use gas to get a Ford moved down the road!
Be sure to let us know what you find out!