Thomas, Isuzu sets the initial alignment with #4 cyl on TDC compression stroke, not #1, thus the confusion. If you rotate the crank 180 deg you should find proper alignment. Note that at this point the dist. rotor will be pointing at the #4 spark plug wire's contact in the dist. cap.
Regarding your crank bolt, I've used the breaker-bar-on-the-frame trick many times and it's always busted the bolt right loose. As you're looking at the engine, the breaker bar would be over to the right, or driver's side, resting solidly on the frame. You can also put a block of wood between the bar and frame if you want to cushion it. All you have to do is 'bump' the key and it should bust that bolt right loose.
When you're doing the gasket replacement, check block/head for straightness as a warped surface will cause problems. Check for proper placement of the dowel 'split' pins, one in front and one in back of the block. These locate the head and it'll jump around on the block if they're not in place. Given the 'high quality' repairs done to your rig so far, it's certainly possible they left them out!
Chase out the head bolt holes in the block with a 12MMx1.50 tap, this'll give consistent torques on the head bolts. Holes full of crud may not even tighten down fully and can cause a blown gasket.
Do use an Isuzu head gasket, not aftermarket, which are more prone to blowing than the factory item.
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is a good source of new parts, as is Isuzu Guru Jerry Lemond in Dacula, Georgia. Jerry was a factory rep and knows these critters inside and out! Great guy to deal with, too. snipped-for-privacy@bellsouth.net
Re-torque the head after 500 and 1000 miles, then do it with every valve adjustment (10,000 mile intervals). You'll have to do the KM conversion, my brain ain't up to it tonite!!!
BTW there are several very active Isuzu groups on the 'net and you can search past posts for more detailed answers to your difficulties:
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HTH............ed '90 Trooper LS 3.4 '89 Spacecab 4X4 2.6 '89 Trooper RS 2.6 '89 Trooper LS 3.1