It seems the only ones that are obvious is the FS designation for four strokes. For them, the F may be for Four Stokes followed by an S for Single and T for Twin.

Moving on to two strokes, I have some observations. The FSR line had Front intake and Schnuerle Scavinging, so maybe it's a combination of Front and the SR as suggested by downunder. Note that while it's possible that the R could have originally been Ringed, they made several ABC FSR engines. Further evidence suggesting that the F stands for Front is that the rear intake engines, such as the VR series, start with a different letter. However, that theory goes out the window when you consider there were several front intake, rear exhaust engines with a VF designation.

After spending 15-20 minutes looking through the 2 engine charts I have from the 80s, I found there were too many exceptions to come to any definite lettering pattern. The following is the closest I could find to a pattern.

F in the first position usually means front intake. However, there are also V designated engines with front intake, so you can't say that if it's not an F that it can't be front intake.

V in the first position appears to indicate something other than a "traditional" front intake, side exhaust configuration. On the V designated engines, the second letter usually identifies Front or Rear exhaust, but I found both front and rear exhaust R designated engines.

R in the first position appears to mean Rear intake.