Tiny Bubbles

[BillK]

Replaced IP last weekend. Starts hard, runs great for awhile, then when warmed up, throws code 34 (injection timing stepper motor circuit fault). Timing must be going into some 'limp home' setting. Goes from measured 9-13 degrees (using Snap-On Mt-2500 scan tool) to 25 degrees and clatters like a big rig (or Ford or Dodge).
Noticed small air bubbles when it starts in morning cold and runs rough like a gasser that is missing a little. Bubbles go away after fuel flows for awhile.

Help--I'm ready to shoot it.
Have replaced the Oil pressure switch and crank position switch.

[gmctd]

Bubbles can indicate air leak and\or clogged filter(s), where IP is starving for fuel.
Check rubber hose connections, filter seals, and filter element.