I'm thinking of taking it out and selling it. Will it affect anything besides GPS? For example will something annoying happen like the MFD keeps switching screens or something?
Agreed, and annoying for a future owner as once happened to me. But no, you can remove it. You will only get an error message if you press the nav button on the bezel or steering wheel. It is not as big an issue nowadays and given that practically no one wants these things, I doubt you'd get much for it. I think $50 might be optimistic.
What's worth more money is the MFD out of the nav car some of those things sell on eBay for $400 a pop but yet the non nav MFD 50 bucks for some reason I think you could just put the possibly put the non nav MFD in your car sell the MFD for the nav without the nav system possibly for a couple hundred dollars or better.
The two MFDs (type 1 and type 3) are not interchangeable, so not really a practical option. Even if it were possible, I wouldn't want to trade down to the Type 3 MFD, personally.
It's not really that I am looking to get money out of it but I'm considering putting a compact amp/subwoofer under one of the seats and the passenger side has the JBL amplifier.