Hello mrbenz,
"check all basic tune-up settings before altering complex fuel injection settings." A simple adjustment or replacement of an inexpensive tune up part will often solve the problem preventing comlex and expensive injection system repairs.
Many times the most complex, expensive and least understood system on these vehicles (the fuel injection) is the scapegoat for every engine problem which arises.
Injection pump rebuilders state that many of the injection pumps sent to them have nothing wrong with them.
The morale here is don't jump too soon.
I would check the linkage adjustment, do a fuel volume and pressure check and double check all tune up settings. Check the ignition timing with a timing light at 3,000rpm.
Replace the spark plugs one last time just in case they have become fuel fouled during the set-up process. This may be the best six dollars you ever spent. You can always save the removals for spares or the next tune-up, if this turns out not to be contributing to the problem.
Make sure that the oil level is correct in your injection pump!
Injection timing on this type of injection not very critical and usually will not cause such drastic problems as you are experiencing. However you may not rest until you have double checked it! So if all else fails, the marks on the injection pump are lined up and the pump is installed with the engine at 20 degrees after top dead center of the compression stroke of # 1 cylinder. Be careful not to install the pump 180 degrees off! Verify compression stroke by viewing the camshaft lobes over #1 cylinder are pointing basically upward when the pointer on the engine is on 20 degrees after TDC!
If you need more details on the above just let us know. Ask lots of questions.
Good luck!
Joe Alexander
Blacklick, Ohio