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Did you remember to take the big nut at the back of the valley off? It's been a long time since I had an engine torn down for head gaskets, but I do remember that I took my IP's off to do it. Don't know if it's necessary, but it worked for me to pull it out.
I did take that nut off and the four bolts on the front of the motor, if I pull the ip do I have to re time it? If so how do I do that?
It'll re-prime on it's own. If you have an electric pump that will make the process faster. If you want to, you can just leave the glow plugs out when you re-assemble everything and turn the engine over with them out for a few minute's worth of cranking. About 30 seconds of cranking to 1-2 minutes of cool down time. With the glow plugs out, the engine will crank over quite fast because it's not working against compression.
Your other option is to crack all the injector lines open and crank until you see fuel weeping from them. Once an injector is weeping fuel from the line, tighten it down. Some bleed out faster than others.
Just make a mark on the IP and the housing, so you know exactly where your timing used to be.
There's three nuts on the housing facing the firewall, and three bolts through the gear that you'll be able to get to by taking off the oil fill spout. That's about it. Just don't take the housing off. Creates a huge headache for figuring out the timing gear.