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.
Best Answer
If you have 2 seconds of good flow followed by low flow there is a restriction upstream. The longer the burst the further up stream the restriction is.
The leak at the ball valve stem, You may have melted the oring or nylon seat that seals the shaft when soldering. The heat deforming the seal causing the leak.
I have had luck removing the nut and handle then the nut on the shaft. Orings are easy and cheap the ones that have nylon sleeves can be a bit tougher to find.
In some cases I have purchased another valve same size and brand and pulled the seal out to repair but most have been orings.