70 dart 470 ci drag car build.

Do you have a stand alone o2 you can beg, borrow or steal? Place it in the side that isn't working and then swap sides with the dyno o2. O2's offen times won't read the same from side to side but should read the same on each side with a no change test. Also low rpm readings with an o2 can sometimes be inaccurate.
Do a couple of no change pulls or just partial pulls if the tune doesn't look right. This might give you either more or less confidence in the readings you're getting now. Not having confidence in the data you need to help you tune makes it tough. Especially on a "new to you" system you're still sorting out.
If you have good fuel flow data and air flow data you should have an air fuel ratio channel to compare to your o2 readings. The numbers might not be exactly the same but they should trend in the same direction ( at higher rpms).
Remember that your o2 reading even if accurate is just an average of four individual cylinders in a collector. And based on the position of the o2 it can be influenced by one cylinder more than another. Also air fuel ratio as calculated by an air flow meter and fuel flow meter is going to be an average of all 8 cylinders.
Spark plug reading, individual EGT temps or individual o2 readings can help sort things out on a individual cylinder bases.
I'm interested in how you are using the oscilloscope on the dyno. I used one years ago when doing tune-ups but haven't used one on the dyno. Are you using it durring a pull or under load?