if you are going to do this, you need to seriously consider the suspension issues.
There are multiple noises.
Front and rear bushings will make a squishy noises when cold and driving over bumps. Sounds like you ran over a coke can. There is no fix for this, sometimes lube can help but it will come back.
Struts can, and might squeak like a bad bed when in really cold and dry weather. This is rare though.
Rear bushings will clunk, you would NEED to get the proper fix for this. Do not screw around with bad bushings, trust me it's a pita.
There was an issue with the strut mounts on ALL protege's. But it gets confused with the sounds the mp3's make. It might very well be needing replacement, but I'm thinking what you are hearing is NOT the mounts.
I've owned the MP3 from 2001 to 2003, then I bought the MSP which I traded last summer. I had both for some time. THe MSP is the better car for more reasons then just a turbo. You have to drive one to feel it. The MP3 however does have the euro spec steering column, and it's crazy sharp handling. The MSP feels looser in this respect but it's marginal.
On Paper there is no contest between a MP3/ES. BUT, with an ES, you don't have any of the suspension issues, and it can look just like an mp3 if you put the money into it. It won't handle like the mp3, but hey...you get a sunroof too.
How were the seats? look at the Vinly, see if it's cracked. Look at the steering wheel see if it's cracking/peeling. The stock shifter was also bad for this but that is obviously gone. Grab the back bumer, get the car bouncing...not easy as the suspension is crazy stiff, but listen to the struts for any squeaks....make sure the car is off of course.