UPDATE:
I'm not getting too euphoric yet but it looks like I fixed it. Yesterday, I swapped Picasso IV cards between A4000Ts but that made no difference. I then started looking at versions of libraries. I got advise a couple threads and years back before OS3.14 when I was using OS3.9BB4 to install THORs MMU. This went very badly and my tower would not boot. I had to swap around libraries but I ended up using 68060.library Version 46.4 05/30/18. I have two versions of this library one named 68060-mmu.library and 68060.library that show the same version and size of 46.4.
The stable A4000T, I never installed THORs MMU. It was using 68060 Version 2.2 Jeff Boyer 07/26/96. I checked both A4000T install disks and this is the original 68060.library that came with both machines. I installed this library back onto the unstable tower and so far so good. It has been stable for several hours now. I have been trying everything to crash it. I have also put both A4000Ts SCSI back to "ASYNC" mode so far without issue as well.
So I had a couple separate issues that was crashing both towers. First, I use Storm C4 and I use Magic Menu. I found on one of the support websites that StormC4 and Magic Menu do not play well together at all. Magic Menu Version 2.30 and 2.35 will cause a collision and lock up the Amiga. However, H&P and Aminet both have the fix for this. It is called "MagicMenuPatch". Once I installed that patch on both, there was no more crashing due to Magic Menu. If you use Magic Menu, I would advise to install the patch anyway. It is just an icon added to WBStartup folder.
http://aminet.net/package/dev/c/StormC_ToolsSecond, the unstable A4000T had the wrong 68060.library and I replaced it with the original Jeff Boyer 2.2 version. For some reason even though THORs MMU was suppose to be intelligent and work for ALL 060s it caused mine to crash randomly. If Thomas is around and would like to explain or have me test for him, I would be glad to.
Another added note is that both original 060s were version 1. I replaced them with version 6. I don't know that really did anything but now I am suppose to have the most stable 060 processor with version 6.