Thanks for the pics. I had forgotten about that particular circ pump system design with the modified Waterway center discharge pump face plate. In reference to your questions about the differences between the two pumps and impellers, etc...
The pump behind the pack is a Waterway Center Discharge pump, which means that the discharge, is directly inline with the suction. It's normal sometimes for the impeller to go slightly out of round. If it drives you nuts though, here's the replacement for it:
Impeller
Your pump #2 is a Vico Side Discharge - (actually looks like a Big Foot pump). Different design and mfgr.
Here's what I'd do to try to fix this.
1. Close down the small ball valve until it's only 1/3 open. (I'd check to be sure that water was still coming out of the heater/filtration jet).
2. Close all jets for pump 2, except the one that's furthest away, and that one leave wide open.
3. Adjust the temperature setting to the lowest possible value. If it's easily accessible, I'd unplug the small grey circulation pump.
4. Start up pump 2, and wait, watch and listen. (Always leave pump 1 off during this procedure)
5. If after a minute or so, nothing changes, I'd close that ball valve down all the way. If no change after about 30 seconds (you'll hear the air and water change as time goes on), I would proceed to the next step.
6. I'd slightly loosen the 1 1/2" pvc coupler fitting that's attached to pump 2 (on top), watch and wait for nothing but water to leak out (yes I do this with the pump running). You have to be very careful only to loosen it enough to make it leak, not more than 1/2 a turn ccw. Tighten it down once it's obviously clear of air.
I doubt you will need to go to step 6. What's happening is that the circ pump is taking the lions share of the water pressure coming from pump 2. That's also why they put in the ball valve - so it can be forced to push the air out of the rest of the system without the circ pump's impact on the system. In any case, it is very important to be sure that the spa's set temperature is set lower than the current temperature of the water. If not, then when you close that ball valve, the heater will boil out very quickly, and you'll destroy your heater. It's either that or disconnect one wire on the pressure switch so it ensures that the spa control won't send power to the heater while the cavity is pressurized with the closed ball valve.
Last thing, the fact that the impeller is a little wobbly isn't such a big deal, but in a marginal circumstance such as this, what will happen is that some of the water pressure in the pump wet end cavity will also find it's way back into the suction part of the impeller. And the cavitation effects don't help either. I'd definitely consider replacing it and the pump seal sometime in the future.
Be very careful with all of this, and let us know how things work out.