questions on new cobra

I don't know about the older cobra's, but when my 04 gets to operating temp. it stays
right in the middle and never budges. Maybe your thermostat is starting to go.

Do you know if your '96 had the "cooling" TSB performed on it? Call up SVT @ 1-800-ford-svt to find out. Also might want to invest in an aftermarket water temp gauge, as the factory ones are not all they're cracked up to be...

Yes, MIL Elims will prevent the check engine light from appearing on your dash once you swap to an aftermarket midpipe - there are the plug-in variety as well as splice in type; I purchased mine from www.ponyexpressperformance.com

In regard to your temperature question---since you don't know what the service history on your car is (at least you didn't say), I'd for sure change out the thermostat and coolant. Also, unless you know they've been done, I'd do the hoses at the same time. Its a fairly easy and inexpensive job that you can do at home and its worth the piece of mind. Believe me, you DO NOT want your thermostat sticking shut and overheating your motor! (ask how I know). In fact, for more piece of mind, I'd probably start a hit list of things to check/replace---hoses, belts, filters, etc. My 3 cents worth