1st and second gear vibration

Just bought a 2001 with 105k miles. 5spd. Exact year I used to have back in the day. That one ran fine. Right off this truck was sputtering out bad with heavy throttle and the worst in 1st and second and had a k n pipe on it that I did not know about from the seller. I replaced the maf and put a stock intake and filter on there and it eliminated the sputtering out. However the truck still vibrates with heavy throttle only in first and second. It seems to go in and out during the rev range. It has no codes it did have P0171 before and after the maf but it cleared sometime after the maf. Power seems fine. It seems shaky some of the time in neutral but could be in my head. I went ahead and cleaned out injectors TB did plugs and wires and a new fuel filter. Prob persists. Mechanic said he thinks its the driveline. It had rust and undercoating could have put it off balance. I find that strange to be the case since its not vibrating unless there is throttle and only in neutral or rev range. Appreciate any help to what this could be.