Hi FE155,
Your air / fuel ratios with stock exhaust were a little too rich between 3,600 and 5,000 RPM where they were in the 10's (mid 11's to flat 12.0 is perfect with the blower). However, now that you have full exhaust with headers, hi flow cats and cat-back, the air / fuel ratio will lean out and get closer to ideal as the engine will do a better job of burning the fuel with the new exhaust. If anything we may need to add a bit more fuel in the low end and take out about 3% in the midrange (or add more timing). Obviously, this depends greatly on the program card you're using. Since you're in CA with 91 octane and a cast piston engine, I'll assume you're running a "S-9D" card. If you were to switch to a "6D" card, your air / fuel should be about right as it has a little more spark advance in the midrange. We'll be glad to make adjustments and send you tweaked programs (by e-mail if you have the VEC2 software for burning your own cards) after you get a chance to dyno again with the new exhaust. Generally, we set the programs up for cars with high flow tubes, filters and exhaust, which can make them a tick too rich on cars without those mods. We should be able to get the air / fuel ratio a flat 12.0 within one or two pulls.
To answer your other question, it's ok to check the ratios at the tailpipe, but your graph will be a little late. What happens at the combustion chamber will then have to go through the entire exhaust, through the air hose in the tailpipe and get pumped up to the oxygen sensor at the dyno module. I've seen the delay to typically be between 250 and 350 RPM based on engine RPM (a graph showing a particular ratio at 4,300 rpm would actually be what happened at about 4,000 rpm). To take the delay out, you have to get the sensor closer to the head.
Regards,
Sean