Andy, I am sorry to hear about your father. Somewhere I saw an engineer drawing of a side view of the diesel engine install vs the wbx install. The diesel install was definitely hanging low in the rear, not level. I tried to explain this before. It was not obvious until I installed the upgraded wbx transmission. I don't know that it is the engine that sits lower as much as the nose of the diesel transmission sits higher. Rather than raise the deck lid entirely, I cut a hole in the cover and made a cap. The cutout covers the oil filter, accessory belt tensioner, the power steering pump bracket, and the injection pump. I had to cut a larger hole when I upgraded to the wbx modified transmission. I also made a new aluminium cap. I think the oil filter could be removed from the block and a remote filter used and then the engine could be drooped even more. This might give you the clearance you need to not modify the engine cover. I am not running power steering, so the pump bracket could be cut and possibley the belt tensioner could be relocated somehow. The shift linkage would need to be adapted as well.
On a positive note, I just returned from a 3000 mile round trip to Wisconsin and back. Zero problems. The new nozzels were just what was needed. I was able to drive up through Chatanooga Tn in 4th gear at 70mph and the cruise set. Hwy mileage is about the same. Coming home, I accelerated up to 86mph easy on the flat, but my wife asked that I save some for the rest of the trip home. I believe 90mph is possible. To those reading this, I believe you will need to increase the power either with nozzles, chip, or both, if you want to regear and have plenty of power for going uphill in a Vanagon camper. Wish I had done it before our trip out west last spring. I don't know how the clutch and input shaft will hold up pushing that box up hill. mark