Motorcycle Questions? Ask a Mechanic.
The Flathead 3 speed drain is just the small bolt (3/8" thread if I remember correctly) located between the two rows of primary chain adjuster nuts underneath the transmission. You'll probably need to get the rear wheels up higher to get to get to it.
You'll remove that bolt to drain, re-install and fill with kerosene (or similar), rotate it a while, then drain and repeat until the flush comes out clean.
I hope this helps. Thanks, P.J.