I'd clean it as best you can, then crank the engine over for a few seconds to blow out any pieces that may have fallen into the prechamber.

Wont this suck the gunk into the engine if the glow plugs are installed? Or are you saying to have the glow plugs removed?

Sorry, I should have clarified... clean things up, then with the glow plugs still removed, crank over the engine. The compression pressure should blow out any debris via the glow plug holes. Nothing should fall into the combustion chamber, because the prechamber is in the way... debris would collect inside the prechamber, and cranking the engine should blow it out. Once you're happy with the cleaning job, install the new glow plugs. I'd put anti-seize on the threads but I thought I remember some mfr saying we shouldn't do that, although I can't for the life of me think why not.

Well I already put anti sieze and installed the glow plugs. I would hate to do this over again. Do you think it would be wise to take them out again?

Nah, if you've already got everything back together, I'd forget it. The intake manifold, and flapper valves, need to be really clean though.

Wel after a few days I am now a bit unsure on where each vac hose goes. Could someone bail me out with some pics or help on where each hose should go on the intake manifold and the cross-over pipe? I would like to make sure they are correct before I install the intake manifold since it is quite tight when the manifold is installed. Thanks again.

Just a note, I would have attempted to look at the EPCOnline for a diagram but I am a MAC computer user and that system does not support MAcs.

You've got air in there--Any fuel leaks after shut down? i.e., a source of air? It takes a bit of idling to run air out of the supply lines after you've opened it up, especially if you changed filters and didn't fill the spin on with fuel?

I didnt change any filters, only the that I previous mentioned RETURN LINE FROM INJECTION PUMP TO FUEL FILTER Part # 606 070 05 32.

Would letting air into the system make the engine smoke so badly and make knocking noises?

Yes, air is a bugger--did you change the two crush washers under the banjo bolt with that line, also, I presume the new line had a new o ring in the recess at the filter end?

additionally, the clear lines around the pump and filter, can you see air in any of them right now?

NO I didnt change anything, I just reused the washers that were on the old connector. Is the banjo the brass end with the hole in it?

yes-on the block side of the injection pump-incidentally, it's more than a bolt, it's a check valve. . .

You are not saying that this line with the banjo end is a check valve are you? I dont see it. Or are you saying that there is a check valve on the injector housing? I dont see any leaks and I dont see any air pockets in fuel line.

Should I attempt to run car again and just idle it until it hopefully clears itself up?

Okay--the banjo bolt on the block side of the pump is a check valve--601 070 06 46 VALVE (Overflow valve) My concern is crush washers and o-ring in past experience have been unusable and tend to leak if reused.

That said, I personally would run it at idle till it's warm and if it clears then give it a highway spin. refrain from running it hard till it smooths out.