My 1999 Ranger 4-speed had its transmission rebuilt last year, before I found Scotty or I would have never done it. Once the truck is warmed up, I still intermittently feel a slight thud under the seat when I'm slowing through 20 mph. My girlfriend doesn't really notice it, but I do. They put 3 different valve bodies in before an initial rebuild problem was solved. It's on the 2-1 downshift. I never feel it when it upshifts, only when braking, and it's not every time. The transmission otherwise shifts fine through all gears. I've never had a CEL/ transmission light come on. 

I've been thinking, could this possibly be related to the slip yoke on the driveshaft not having enough grease? My truck has the infamous low frequency shake the Rangers with slip yokes have, but not all the time. When you initially accelerate from a stop and the slip yoke isn't greased properly, the trucks have a very subtle, low frequency vibration that stops within 5 mph. I greased mine last year, it could be time again. My thought is the driveline isn't under load for that shift when you slow down, so the yoke could slip and bind up with the gear change altering the torque/ RPMs. My only other thoughts are a sticking 1-2 solenoid or valve in the valve body.

Thanks for any ideas/ opinions!