I just redid my head gasket on the 1.6 NA hydraulic lifter engine. Took the head totally apart and cleaned all the valves, checked the hydro lifters, and inspected seats. Everything checks out and put it back together. I put the 1 notch fiber gasket on there and torqued the head down according to Bentley manual procedure using new German 12mm head bolts. The pistons were at half way so there wouldn't be any valve-piston interference. Then I did the mechanical timing of the valves, pistons, and (Performance Diesel) injector pump. Got the pump set on 0.95mm (about 0.038 in). Turned everything by hand to make sure there was not any interference. I also took apart the injectors, cleaned them, and torqued them back together to spec (70 N m)
When I started the motor up, it was running like it was on 2 cylinders. Actually, the #1 piston intake port was huffing and popping out exhaust, but the engine did run extremely rough. I did a leak-down test on cylinder 1 with a tool that I made from an old injector body. The piston was at TDC and the cam was in the closed position, but I had 100% leak out of the intake manifold...
So I took the head back off to see what had happened. I was expecting to see a broken valve, broken lifter, or something. But there was nothing apparently wrong! Interestingly enough, #2 and #4 cylinder were black from the brief combustion, but #1 and #3 were totally wet with diesel fuel and evidently NEVER GOT ANY FIRE! So #1 and #3 looked exactly the same, however only the intake on #1 was back-firing through the intake port. I'm absolutely stumped.
Is it ok to re-torque down the head with that same head gasket, bolts, and torque procedure or do I really have to buy 10 new bolts and a new head gasket and just hope for the best?
At a high level it sounds like your pump might have been 180 degrees out... injecting fuel but at the wrong times. Do you have the pump sprocket with two possible holes for the locking pin? In any event, at TDC the key on the pump shaft should be pointing towards the head at 9 or 10 o'clock.
Having said that, the part of your story I don't understand is having 100% leakdown on #1 intake when you could see that the valve was closed. So, it may not be that simple after all.
And yes, the head gasket and head bolts are single use only... once torqued they are permanently deformed.

Lots of folks upgrade to studs for this reason alone.
It does sound like your intake valve is leaking[not seating properly] try measuring for excess valve lifter gap.
Also pop test your injectors. Its so easy to overtorque and distort nozzles so that needle sticks open.
Have the head pressure tested to make sure valves are seating and sealing. Get the injectors run on a flow bench(or pop tested) to confirm that they are operating correctly. Do not recycle headgasket or bolts as they are torque to yield. BTW why did we have the head off originally? Cheers.
Bad injectors was my first thought. Timing being 180 off is also very possible.
Next time you do a leak down test and get back results like that, remove the cam and test again. If they are still bad then use a wooden dowel and hammer and hit the lifters to try and get them to seat and then retest.