Exhaust Some issues resolved but still running bad

So I just took notice of something. The old platinum plugs that came in the car were only gapped to .040 and the new copper ones I bought were also at .040 so i, like a dumb ass, just installed them. I read that gap should be at .054ish. Could this be the cause of some of the bogging down after 2,000 rpms? What issues might this cause?
 
Until you do the checklist you are stabbing in the dark.
So I went in and properly gapped all the new plugs. The cap and rotor I got were garbage so I returned it and have a motorcraft on the way. MSD was horrible and making the car sputter and misfire after 2,000. I put the old cap and rotor back on for now and it runs much better. So Im still waiting for a new O2 sensor harness, O2 sensors, all new injectors and ignition coil. While I'm doing the injectors I'm going to get back there and change the PCV valve and clean and tighten that HEGO ground wire. So as it sits right now. I did have code 33, 41 and 91. Then after some work I retested and got 31, 41 and 91. I erased all those codes and drove for about 20 mins and got 13, 31, 41 and 91. So I thouroughly cleaned the IAC and I also sprayed some electronic cleaner on the TPS sensor harness. After hooking everything back up I drove for about 30 mins dumped codes again and 13 was gone but now it has 32, 41 and 91. Any idea why that EGR code keeps changing? Also, when setting my timing, after it was set, I unplugged the IAC connector to see if it had any effect and it literally did nothing. Car idled exactly the same. Of course it's a bit too high around 850 rpms but it stayed steady.
 
Until you do the checklist you are stabbing in the dark.
So, I've gotten I'd of code 31. Still working on the others. Anyway, I've changed out my cap and rotor twice and each time it runs horribly. As soon as I put the old one back on, it's much better but still not perfect. Do you think codes 41 and 91 could effect this? Or what are your thoughts? It's a motorcraft distributor and I tried motorcraft and MSD cap and rotor and both of them caused the car to not run above 2,000 rpms. I've also done, pcv, no vacuum leaks, all hoses changed, new ignition coil, wires, plugs and new fuel injectors. Fuel pump and filter are good and fuel pressure is 33 with vacuum and 41 with vacuum off and plugged.
 
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Yuup, slowly running through it. The car runs really great and idles great, TPS is on point, I've also done, pcv, no vacuum leaks, all hoses changed, new ignition coil, wires, plugs and new fuel injectors. Fuel pump and filter are good and fuel pressure is 33 with vacuum and 41 with vacuum off and plugged.
 
Only thing I haven't checked is the computer connections. I'm worried about hooking a multi meter up as I've never done electrical stuff before.
 
So I'm curious, I started with my car having a 29, 31, 41 and 91. I've since gone through almost everything that might cause these issues short of checking the computer pins. I don't want to mess anything up. I still has the smog pump and charcoal canister. Anyway, I've replaced every vacuum line in the car, I put on a new EGR and position sensor, I've replaced both O2 sensors with bosche and also replaced the O2 wiring harness. It definitely needed it as the old one had been cut into, I removed the upper intake and replaced all 8 injectors with factory 19# injectors. I installed all new gaskets for the upper intake. I've done Ford wires, copper motorcraft plugs and a new motorcraft ignition coil. I've done the radiator, fans, thermostat and water pump. No more overheating. I plan to just install a new speed sensor and cable as the speedo doesn't work at all and my goal is to eventually have almost all new items on the car. So....after all that work I was able to get rid of code 31. I'm still stuck with 41 and 91. After changing the O2 sensors yesterday I noticed 41 went away but came back today. So, short of checking the computer and thermactor tube for clogs I think I've done everything. No more gas smell or overwhelming smell of exhaust. The car runs a ton better but still has a few issues, it sputters like I hit a rev limiter at 4,000 rpms and I've tried 2 different cap and rotors, when I put the new ones on it does the same hesitating and sputtering but at 2,000 rpms. When I was doing the O2 sensors yesterday I also noticed that I definitely have aftermarket exhaust and only one cat per side. Whoever installed it routed the thermactor air tube to just the passenger side cat and hooked it straight up to the cat, not before it. There's also a leak in the thermactor tube before the cat. Could the leak, or the fact that it's only hooked up to one side be my problem? Any other advice would be greatly appreciated. You have definitely been the most helpful person on here. Thank you!
 
So I'm curious, I started with my car having a 29, 31, 41 and 91. I've since gone through almost everything that might cause these issues short of checking the computer pins. I don't want to mess anything up. Not very electrical savvy. I still have the smog pump and charcoal canister. Anyway, I've replaced every vacuum line in the car, I put on a new EGR and position sensor, I've replaced both O2 sensors with bosche and also replaced the O2 wiring harness. It definitely needed it as the old one had been cut into, I removed the upper intake and replaced all 8 injectors with factory 19# injectors. I installed all new gaskets for the upper intake. I've done Ford wires, copper motorcraft plugs and a new motorcraft ignition coil. I've done the radiator, fans, thermostat and water pump. No more overheating. I plan to just install a new speed sensor and cable to correct code 29 as the speedo doesn't work at all. So....after all that work I was able to get rid of code 31. I'm still stuck with 41 and 91. After changing the O2 sensors yesterday I noticed 41 went away but came back today. So, short of checking the computer and thermactor tube for clogs I think I've done everything. No more gas smell or overwhelming smell of exhaust. The car runs a ton better but still has a few issues, it sputters like I hit a rev limiter at 4,000 rpms and I've tried 2 different cap and rotors, when I put the new ones on it does the same hesitating and sputtering but at 2,000 rpms. When I was doing the O2 sensors yesterday I also noticed that I definitely have aftermarket exhaust and only one cat per side. Whoever installed it routed the thermactor air tube to just the passenger side cat and hooked it straight up to the cat, not before it. There's also a leak in the thermactor tube before the cat. Could the leak, or the fact that it's only hooked up to passenger side be my problem? Any other advice would be greatly appreciated. P.S. I also have an A9S computer not sure if they're more sensitive to lean or rich codes being a California computer? IDK
 
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Well, as it stands right now. I got so pissed that with everything I was still getting 41 and 91. As I said before the thermactor tube was leaking exhaust because the previous owner(s) installed a complete exhaust minus headers and had cut into the new cat and welded the thermactor tube to only the passenger side cat and left the two tubes just dangling with no actual seal. So it was leaking exhaust and letting in a bunch of air. So I removed the smog pump and all the related tubing, plugged the holes and crimped the exhaust tube. Low and behold, no more codes. I went on a two hour drive tonight and had no issues other than a bit of hesitation at about 4,200 rpms. I'm going to weld that tubing tomorrow as its only crimped now. In the next month I'm removing the cats so no big deal there.
 
Any ideas anyone? Everything for the fuel system and ignition system is new besides the actual distributor, pressure regulator and the TFI. Still hesitating and sputtering at 4,000 rpms. All codes remedied. New fuel pump, fuel filter, fuel injectors, cap, rotor, wires, plugs, pressure regulator is holding it steady at 41psi, new ignition coil, all new vacuum hoses, new EGR and position sensor, new PCV, valve screen and grommet. Just a bad cylinder or could it be distributor it self or tfi? Anyone?
 
Side note, dumped codes. Got nothing but 44 and 94 CBT came back 9 across the board.