Several problems with 2008
 

Hello everyone. First let me say I'm new and I'm sorry if any of these issues are covered anywhere else. I'm also not super mechanically inclined, so please keep any answers relatively easy to understand for a non-mechanic.
I have a 2008 automatic transmission Mazda 3 touring. It has almost 85000 miles and has given me relatively little trouble. A few months ago I drove through some high water and it caused the TPMS to malfunction. I have since had the tires replaced, sensors checked, reset, checked again, reset again, etc. The sensors are good and working so the issue is with their communication with the computer. Around the same time my key fob stopped working. I have tested the batteries in both key fobs and they are in good working order. I just brought it into the shop because the check engine light was on and it needed a valve canister assembly something or other replaced. They told me that the key fob issue and the TPMS issue are related, something to do with the computer or some kind of module. So, in layman's terms, can someone explain to me exactly what this module is and what kind of damage am I looking at to have it fixed? The shop told me that just the computer part alone was around $800 which I find obscene.

Additionally I do have the motor mount issues which causes vibration when I am in Drive but stopped. I don't have any vibration when in drive and moving at any speed or when in neutral or Park. And of course because when it rains, it pours, the window assembly on my driver's side door has failed and my window is off track. I can jimmy it closed if needed. I'm pretty sure my roommate can fix the window assembly, but is the motor mount issue very critical? It's been vibrating for at least two or three years now.

Thanks in advance and sorry for being a noob.