To tell apart an Aisin equipped 3500 from a 68RFE equipped one, look for where the transmission dipstick is. If the dipstick is on the passenger side, then it's a 68RFE. Aisins have the dispstick on the driver side. That's the easy way to tell without getting on your knees to look under the thing. 
But if you want to be doubly sure, the Aisin units also have PTO covers on the side of the transmission. 68RFE's don't. That was the 2nd reason to get an Aisin, if you needed the PTO option for anything like running hydraulics and such.
My 3500 is a 68RFE equipped unit.