yeah at this point if you did not find anything loose, or damage to anything and it stopped vibrating it's time to let it run and see if anything else shows up later on. Hopefully if it does it wont be serious.

hello, followed suggestions and checked out the hyd pump and pulley, also checked on flex plate and all looks ok. also checked ignition wires and they are ok. will replace aftermarket wires with OEM anyway but for now engine is working well. one thing operator told me was that when it started shaking or vibrating he gave it more gas and the vibration went away. i was not able to duplicate vibration while performing troubleshooting and following suggestions. for now, since the units is running fine i will wait for it to start acting up again unless somebody has another suggestion.

if you found nothing between the engine and hyd pump area wrong i would pull the cover off the top of the flywheel housing and check the flex plate on the torque converter and make sure it is ok, may have a broken flex plate. (this is common on these units but is usually accompanied by a noise when running coming from the flex plate rattling)

if nothing is wrong there it might of been a cylinder not firing correctly and engine missing causing the vibration, then something let the cylinder start firing and that might of been the clunk you heard, maybe a small backfire or something... when all cylinders started firing again, it smoothed out.
Bad wires can cause this.

pulley that is between the crankshaft and the hydraulic pump, on the pump side.