P0216 b

My 98 has been sitting for a couple years, dragged it in the shop to get it going.
1-Replaced both batteries, cleaned the cables
2- replaced the lift pump as it was dead
3-replaced fuel filter
Had to use 4d40 to get it fired up, but it eventually started, running rough and smoking bad.
After running it for a bit It runs smooth now at idle and driving it slowly around the shop but you can hear the engine clatter get loud then back to normal. I cleared the code and it’s still off but the engine noise is still there coming and going.

P0216 is unable to stabilize the injection timing, or the timing is physically too far off for the PCM to compensate. First, make sure the pump is secure and not wandering around while it's running. Other than that, it could be air still trying to work out, or something just sticky from sitting. It would be a good idea to check the quality of the fuel (or simply replace it). The fuel doesn't sour, but a couple years is a long time for other things to do bad things. Also, check for rodent damage, just because. Get it up to operating temp and let a couple/few warming cycles work out what it can.

I’m going to drain the tank this weekend to eliminate that and I’ll check the wiring, thanks