Sorry to hear about your "odor" problem. Maybe there is a local public fountain you can take a dip into!!!

However, the problems you describe are fairly common, but may be tricky to isolate. Let's try some basics: Relieve the pressure from the bladder completely. Let the well pump fill the tank completely and bleed any air from the system using the faucets with the pump running. Again, with the tank full of water, close all outlets and charge up the bladder to about 60PSI. Most systems work fine between 45 to 65 PSI. Anything over 70 is pushing it. The tank needs to be charged when full, not empty. Monitor the pressure as you draw water. Does the pump kick on constantly when the pressure reaches the low limit, and off at the high limit? This will help tell if the regulator is working properly.

Is there any pulsating water pressure at the faucets?

When you are sure you have a full tank, no air in the system, is your second floor water flow ample when the tank is reading 60psi?

There are a few "if's" here. Depending on how the pump behaves and the pressure responds, you have to determine if the problem is with the pump and volume of water being delivered to the tank, or if the pressure regulator is properly operating.

If you are still seeing any pulsating water pressure at the taps, then the bladder is water logged again. If the bladder pressure drops too quickly, then most likely the volume of water from the pump is low. The pressure should remain fairly constant at the tank if all the functions of the pump and regulator are working properly. Good Luck

I think you have two completely separate issues that you became aware of at the same time, and which are mostly unrelated.

Improperly set system and air pressures in bladder tanks.

A note - the higher the system pressure, the less water storage (drawdown) in a bladder tank. So you might get better performance from a 40/60 or 30/50 setting.

You are also at risk of damaging the bladders by underfilling the air for the pressure you have set on the water side. The bladder becomes much more distended than it's designed to be, and lots of water simply sits in the tank with the effective volume of the tank greatly reduced, since the first water to enter the tank is raising its air pressure from your too low setting to where the pressure switch is set, and shrinking the air bubble to do that.

Low pressure on the second floor bathrooms is probably from a blockage.

Pressure due to elevation is 2.3 feet per PSI, so pressure on the second floor due to elevation is probably not really the issue (might be 8-10 PSI less than the basement in a typical house) and of course it worked fine until you drained the system; so it's not "really" pressure loss, in the sense of the pressure in the pipes - IMPE it is often the case that when you drain and refill a water system "crud" (usually harmless, but unappealing, deposits from the water) in the pipes gets knocked loose with all the bubbles passing through and will plug shower heads and aerators - that does cause pressure loss OUT of the showers and sinks. Try removing shower heads and aerators, cleaning them, and blowing the pipes clear without having them in place.

I would suggest draining the system again, verifying that the air pressure is still 38 (if not you may have a leaky bladder) and resetting the pressure switch to 40/60 (with a typical pressure switch, be sure to turn the pump breaker off before adjusting.) Then remove all showerheads and aerators, repressurize the system, and blow the pipes clear before reinstalling the cleaned showerheads and aerators.