OBD II - on board diagnostic's, cannot be cleared by removing the battery terminals. That was something that only worked on the earlier version of vehicles.
Before OBD II - you had a plug for each manufacturer and computer for each vehicle. A technician / garage had to have on hand a computer program for every year, make and model of car and a plug to adapt their scan tool to the port. I had a Snap On scan tool for years and it cost about $500 per a year - just to buy the updates and plugs.
Finally the manufactures all got together and agreed to one simple plug and one simple program for all vehicles. I will not say that it was all a scam, because the earlier vehicles usually had terminals that could be jumped, where a light in the dash board would blink and you could count the blinks and figure out which codes were coming up in the computer. Those computers could be cleared of their codes by removing the battery wires and maybe even dead shorting the terminal ends on the wires together - which would remove the residual power which was held in the memory - usually in a capacitor.
The OBD II did away with all that, but required you to have a scan tool to read the codes and to erase the codes from the memory.
Power tuners are a poor substitute for a scan tool.
Changing the program from the origional or upgrading your exhaust to a aftermarket - could void your warranty. What that means is that it could cost you mucho denero.
One little guess - is that the aftermarket exhaust did not have bungs for the down stream O2 Sensors or that they were damaged when they were removed or that the mechanic who did the work removed the cat's.
You are there and I am here and I am just taking wild guesses as to what your problem is - without the proper codes and not being able to see your vehicle or know what you did to it, would be like me calling a physician and asking him / her over the phone - what is wrong with me? - without describing the problem and without a office exam - it is pretty tough.
100 miles isn't going to hurt it, and driving without the down stream sensors will not hurt it either.
Here is some of the codes
http://www.obd-codes.com/trouble_codes/