I assume you got a new head gasket
The cracks in the head are common. Mine had them as well and the shop "stitched them" I guess they drilled patterns across the cracks and then welded the groves. They were tiny, magnaflux would reveal them but i wasn't sure where to look. They were in the pre-combustion chamber passages between cylinder 2 and 3.
As far as that third IP bolt, everyone seems to make a special adapter. I use flex extension and adapter to my 1/4" drive ratchet. Ends up extending just above the heat exchanger
. The more you do it the easier it gets.
Don't over tighten the high pressure lines. They need to line up so that you can hand tighten the nut. Otherwise you might strip a nut or scar the mating surface.
Also don't forget to re-torque the bolts after 25-50 hours in correct order. I am on hour 30 after a rebuilding the engine this spring. I was amazed that i got 1 to 1-1/2 turns on most of them before I reached the required torque. That of course requires taking the rocker off. Not that big of a deal if you have good access.
Injector nozzles are a rip off. I got a 650$ bill for changing nozzles and pop-testing the injectors. I am not even sure if they changed the springs.
Ebay has the nozzles at around 30$ per. I also found a chinese supplier that sells them for $3 but minimum order is 30.