Hi, first congrats on taking a risk and making it work! for $45 a new screen is really great. I recently bought a MSO 4104 at an auction where the scope powers up but then overheats and fans were not working; two SMT fuses replaced, and ... voila. It was also missing the pan/zoom knobs, which was an obnoxious $70 including $25 shipping from tektronix, but this whole endeavor was the deal of a lifetime probably. I'm not sure I'd have been as brave as you to get something with a dead screen.
About the modules.
There was a seller on ebay who was selling "empty modules", for the MSO/DSO 4000 series anyway, something like 4 of them for $150 and with such you should be able to transfer them out of the scope and then back in again.
But - I'd guess it is unlikely that a firmware update would erase such modules, b/c tektronix would have so many people furious if they did do that with no warning.
FWIW, the MSO4104 has a later version of the FW than I was able to find on tektronix's website of all docs for the series. Curious.
Have fun!
J