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.
Assuming metal pipe, I'd set it to about 60, because that's a good compromise between too-high pressure and disappointingly little pressure. That's what most well pumps I've seen are set for, and significantly less than most municipal water systems (I've seen one city water system that delivered 125psi to the house). Much lower than 60psi and you'll be frustrated by the slow flow.
With resilient (not PVC/CPVC) plastic pipe, I'd go a little lower than that because unlike metal pipe, which has very strong, secure connections, plastic pipe has only clamp-over-plastic-over-barb connections, which can fail more easily than metal pipe. With PVC/CPVC, I'd go even lower because it gets brittle with age.
Best Answer
In responding to this, I am including information from your original post. (You said your well is about 100 ft from the house, that the storage tanks are next to the well, and that your plumbing is mostly PEX.) I am assuming that your house is not elevated far above your well. If it is, then you will have roughly 1 PSI additional pressure loss for every 2 ft of elevation.
PEX is sold using tubing size and not pipe size, so if there is 100 ft of 3/4" PEX connecting your well to your house, then the ID of that tube is only 0.681 inches and the pressure drop may be very noticeable. Running two fixtures or flushing a toilet while running a sink might cause 10 psi pressure drop across the run length. If the house is piped mostly with 1/2" PEX, then there would be additional pressure losses there also.
Instead of setting the system operating pressure ever higher in an attempt to compensate for this, I would suggest correctly setting the air charge in the storage tanks for the reason I mention in my comment under your post above, and then use a couple of inexpensive pressure gauges to measure the pressure at various points in the system to locate the losses. For example, use the pressure gauge at the storage tanks, put another gauge at a spigot on the side of the house, and another on a sink in the house. Turn on a tub and a couple faucets and record the pressures. If a significant amount of loss is between the well and the house, then replace that line with a larger size.
40-60 PSI is the upper operating range for many residential well systems, so I would not increase the system pressure above that if the issue can be practically resolved some other way.