Sounds like a bent shifter fork from someone beating it into gear (not you necessarily). As the tranny heats up a shifter fork that is bend to begin with could warp far enough to not properly engage the gear dogs. Frankly, you shouldn't need to "hammer" a shifter that is a last gasp to get home with damage, tranny or clutch. I'd change the oil, filter, and drive it like a little old lady and see if it shifts nice when being babied. If that turns out OK, you and minimal tranny damage, but will still require open surgery, but less broken/bent bits.
Farkled probably WAY too much, but good 20' footer for sure. '96 KLR
, '06 HD VROD, (girl friend hauler
), '05 HD Electra-Glide, heh it's a HD and I'm old now ;-) and I'm proud of riding a 800+ pound bike at my age :-)