lifting the cab to do a hpfp and then to do studs etc are not the same thing, the money difference is quit large. the pumps carry a 2 year warranty from ford so as long as the tech is up on his paperwork getting a pump replacement is not that big of a deal down the road if it does happen. I would be more irritated if I cheaped out by just doing the updated harness and then the pump failed 2 months later.
-the downpipe is not that bad if you are leaving the truck stock.
-egr sounds like it is already gone so shouldn't be an issue
-uppipes and manifolds should be checked for blown bellows, this I can agree with as the stock up pipes are pretty hateful and most shops will want to pull the cab back off they need to be replaced
-ported intake/new oil cooler etc. can all be done with the cab on, if its a stock turbo'd truck its not going to be a huge difference with a ported intake.
-to do the oil cooler intake manifold etc would need to be removed. to do the hpfp everything can stay in tack
I would pull cab, do the new style hpfp harness, new hpfp,new frp sensor and check the uppipes and be done with it. all the extra's are going to cost a lot more money. as far as the aftermarket fuel system, id go with something like Midwest or someone has, I would shy away from airdog and fass because of the high failure rate (from experience) changing a fuel filter isn't that hard and the filters are on the shelf of every ford dealer.
also make sure he gets a turbo mount kit and new exhaust gaskets if your up pipes are fine.
4wd w/cab off time is 11 hours
4wd w/ cab on 13.9
those times don't include diag obviously.
just depends on how much you want to spend.