I've got a C5 Mill, and a C6 Lathe I'm still working on.. But, they both run DOS. And DOS is most likely the limiting factor with your file size limitations. I've seen some previous posts from Sportybob talking about memory extenders or some other special DOS black magic he's used on these old machines. You can probably look at the AUTOEXEC.BAT and CONFIG.SYS that Sportybob worked on and might be able to replicate the file size upgrades on your old C5 machine. You might have to buy more memory for it, but Memory is cheap and fairly easy to find on eBay. I'd also recommend a ChipOnDisk or DiskOnModule upgrade as well. These kind of modifications are relatively easy to perform, but you'll have to know how to work in DOS.

As far as upgrading the C5 to a C6, I think the software is completely configurable to adapt any controller to any machine. I've also got a feeling it wouldn't care about the panel either. Interestingly, my lathe boots and up and displays, "BAD V" for the control panel. The problem would be the pinouts for axis/IO as well as the drives might be different. I vaguely remember doing some searching a while back and seeing something about the single-board motion controllers use different drives from the multi-controller cards.

What are some of the difference between the C5 and C6 controller?

Also, How did you add rigid tapping to the C5 machine? What VFD do you have? Can you just add an encoder to the spindle?