So basically you changed 3 things, and then noticed the problem. Start by checking out each of the 3, not chasing everything else under the sun first. The exception would be the throttle linkage, if by chance you jacked the rear of the vehicle up under the engine and caught the linkage, but bending the throttle sounds like a stretch to me unless you had the jack way up under the transmission or something stupid.
You car will be safe going back to the stock chip with your new exhaust and I would start there. Nothing to lose- see what it does and how it behaves. If it goes back to normal- there you go. A more open exhaust with larger tip diameters (or not) may sound raspier/throatier/louder and pop more. Get used to it.
O2 sensors are fuel trim devices that adjust the chip's fuel map slightly one way or the other to optimize power and fuel economy. When you start your car, the 02 sensor is ignored for the first 60 seconds or so anyway. Completely disconnecting it will put the computer in "open loop", which will not hurt anything except a bit of fuel economy and some optimization of the mixture. Not a big deal. Try completely disconnecting it and see where you're at. Euro Carreras of the 80's don't even have 02 sensors...
My experience: continuing to lean the engine out will also cause exhaust popping noises. You need to find a shop with a "wideband 02 sensor" (specifically ask for this on the phone, if they go "huh?" hang up and try elsewhere). This is what the LM-1 and LM-2 are that 88-diamondblue speaks of. This will tell the tech right away where the base mixture setting is and it can be adjusted via the air bleed screw that is hidden underneath the AFM (it is a 3mm hex). Do not dink around with this screw until you have the wideband meter hooked up.
Steve's chips are generally very good ( I have done 3 with him) but they assume you have a properly adjusted, well tuned engine.
Good luck
BG