I guess we'll need someone to code an application that will be able to sign the files.
I would think this would've been a bigger focus than downgrading, with having the master key.
If we were able to sign files, and have the downgrading that we do now, couldnt we theoretically do this:
Get to FW 3.41
Jailbreak it with a device
Sign the applications and then Install all Applications we want
For the time being, upgrade back to 3.50 (since we can safely downgrade)
Run the Applications without being Jailbroken!
On another note couldn't we make some homebrew like the Wiis homebrew channel that allows us to install packages? We could make it, and sign it (if it isnt already out there, i dont know), and then leave it on our system and just upgrade firmwares.