Jim answered the oil pan question, but I want to comment on your "head shaving." Remember, this is a diesel with a CR over 20:1, not an SBC with 8:1 or 10:1. Don't mill ANY off the head unless absolutely necessary for straightness, and it probably won't be necessary, this is an iron head.
The combustion chambe is so small, that the tiniest cut will drastically raise compression which can rapidly get excessively high.
I agree that the pump is expensive, but so is this engine. I would replace it.
Final comment. I am probably the Maverick on this site when it comes to sleeving versus boring for new piston fitment. The pistons in ANY diesel engine are highly stressed. I prefer to replace them with oversize and just bore to that oversize. If you insist on reusing them INSPECT THEM CAREFULLY. I have seen ring land failure and other maladies.
If it comes to replacing pistons, there are two types. The piston type is determined by the prechamber type, so make SURE they match.
You did not mention the timing chain. Check for stretch before disassembly. If it is stretched at ALL, this is the time to replace it. Also inspect the guide rails closely.