The Protege 2.0L is officially non-interference, however, on this forum after timing belts have failed most people have replaced them without a problem. However, there are some reports of bent valves after a timing belt goes. It seems under most circumstances there is no valve damage but in...
Looks good. An alternative is to get an ES trunk out of a junkyard. Of course, standard Mazda rust is a major issue around the mounting points of the spoiler to the trunk.
That rattling from the rear means you need either 1) new swaybar endlinks or 2) new strut mounts. From rockauto.com endlinks are ~$20 each and strut mounts are $20-25 each.
Very strange. The metal must be coming from the cat, not sure where else it could originate from. It's probably not from the EGR itself. Do you have a picture?
Good plan to hang on to it. Seems here in the northeast, rust kills Proteges before serious mechanical problems. I wouldn't spend money trying to extract more horsepower... the Protege is best appreciated for its handling. If you were interested in spending the money, a suspension upgrade would...
The infamous rear clunk was on the Mazdaspeed Protege. As 03protolx suggested, on the regular Pro, the clunk is the strut mounts or the sway bar endlinks.