This is my best guess..
The way our petcock is designed, the normal ON setting has a tube that extends up into the tank, and only allows fuel to flow when the bike is running. The PRIME position is flat against the top, lower than the normal ON and allows the tank to empty fully regardless of it the bike is on or not.
In pregen bikes, I believe this setting is what gives them the RESERVE, that last gallon of gas after a sputtering "you are almost out of fuel, idiot".
That *might* explain the sputtering to a stop and only putting in 3.8-4 gallons. The last gallon was below the normal filter. Or the filter is clogged?
I ran into this once when my bike sputtered to a stop about 30 miles sooner than planned. Flipping to the Prime got me to the station and about 4ish gallons added. Just make sure you turn it back to ON before you park for too long, else you might find all that gas now on the floor.
I'm clueless on how the choke works, so someone else will have to answer that.