I see we’re of about the same vintage. I bought my first Mac in '89. 
I didn’t know that the Mac Pro 6,1 was an SSD card. Silly really but if it’s like the MacBook Pros with the same, they can be switched out, but it’s not a simple operation. You can also buy empty drive boxes to put the old one in, or just use a SATA cable and a rubber band.
If you decide to bite the bullet on the drive, I’d re-format and install a clean Mojave, then use Migration Assistant to move your User Account across from a TM backup. I would guess that the problem you had in the past was that newer versions of the OS puts things in different places to the original installs, so moving stuff across doesn’t always work. So I’d prefer in this situation, to not move applications and instead, to re-install them with the latest available installers. The danger is that some apps, that have survived OS transitions, may not have updated installers to handle the process correctly on recent OS’s. I actually use 3 generations of Macs, which cater to current, plus 2 generations of depleted software, which I still use. One for a 90’s imaging app, which runs like lightning on a G5Quad running 10.6 for Classic (MacOS 9) and another with 10.6 for a high-end digital back, which is still producing the goods 12 years on. So, similar to the discussion about FW8 and it’s compatibility for FW7 files … I see no great urgency. If it can do it down the road, it’ll be great, but I’d personally rather that precious resources be spent on features, stability and bug removal. However, I appreciate that people working in video, sound and imaging, tend to have a lot more computers hanging around, than the average pro user.
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