[shorod]

Welcome to the forum!

I don't have suggestions for all of your questions, but I'll provide my advice for ones I have suggestions for.

Rust on the bottoms of the doors has been a common issue for most Ford products, and really most cars these days, not just Fords.

The squeal at start up could be a belt, or could be an Idle Air Control (IAC). Not being able to hear the noise, it's hard for me to give a better suggestion than that.

I would expect you'll find the wiring for the CD changer in the trunk on the lower left side (as you're facing the trunk) if your factory deck has the CD changer controls.

I'm not real sure about the 2001 specifically, but are there handles in the trunk to release the seat backs?

As for the remote starter, the only way I'd understand the window needing to be down for the remote to work is if the window has a metallized window film on it. Are the windows tinted? You might be able to get by with relocating the antenna to improve the range. Battery could have an impact, but shouldn't require a window to be rolled down. Or, if you want to go with a new system, get one with a Frequency Modulated (FM) remote.

-Rod