3,4,5 gear engine runs "rough" or seems to shake or vibrate a little. replaces air filter, plugs,wires,dist cap rotor, any ideas

 

Your "drivetrain" incudes the transmission, transfer case, ot "t-case" people call it, and both your front and rear axles.

Persnally, i'd start with a tire blance/rotation, to make sure it's not just a tire out of balance. Many out of balance issues can only be felt at certain speeds.

Other than that, check the fluids in your trans, t-case, and both pumpkins {differentials} to make sure you aren't grinding metal on metal.

Keep us posted, always check the easy stuff first {fluids, tires}.
After that, might be the driveshaft.

Good-luck.

 

Year and tranny model(if known) is helpful... But saying 3,4,5 says stick.
Sounds like a clutch issue being the higher gears, you will get slippage there at low speed with a worn out clutch. A test you can do for a worn clutch is to get up to a steady 2500rpm in 2nd gear and then shift to 5th, if there is lots of stumbling and shuddering or stall you may need a clutch. Another way is to feel for pedal play, a good clutch should begin to engage about two inches from full depress of the pedal, a bad one near the top and a used one somewhere in between.