2005 about 400k miles. Installed aftermarket cat and O2 sensor about 100 miles ago. Been going very well.. Then today it shudders going up hill with cruise set or driving with pedal. Then it stumbles a few times to get back to making power, then seems to get back on its feet and make it up the hill. Don't really notice much on smooth ground. I also noticed the fan seems to run loudly which ice never noticed before. No CEL and not sure where I should begin
If it were misfires you should see the master warning light (red triangle) flash rapidly. You didn't say that was happening. The only other thing to guess at is pinking or some other engine-related problems. Do you have any trouble code to share? Even without lights on the dash, there might be some pending or history codes available. That would eliminate the guessing, or at least cut it down dramatically. If you don't have a scan tool but there are dash lights on, see this post for more information on how to get trouble codes.
I have techstream. No codes. Attempting to drive it 100+ miles tonight maybe that will set off some codes.
I am not sure the master warning light will flash rapidly for a misfire. I think it's the check-engine light that does that. Not for every misfire. Based on the RPM and load, the ECM calculates the amount of unburned fuel going into the exhaust because of the misfire. If it would be enough to destroy the catalytic converter, it flashes the check-engine light. If less than that, it just lights the light.
That new O2 sensor may be running the engine a bit lean. That being said; check fuel trim #'s, fuel pressure. Have you done a leak-down test on each cylinder, of that well worn engine. Has the fuel pump or fuel filters ever been checked, when was the last time you ran injector cleaner through your fuel system?