Domush, I know you said you checked the rods for straightness by eye, but I think you should look into that again/more. Car Doc and others besides me think that is the problem, too. It won't take much of a bend to screw up the alignment, and it would be easy to miss by eye. The pistons should come off the rod pretty easily, and the trick about a piece of glass or granite counter section as a flat surface would work well here.
In my view, if you put it back together and try to run it, it can't last very long. The tight bearing is worrisome, and clearly indicates a real problem. It used to be fairly common to have machine shops recondition rods; I haven't had that done recently, so don't know what it costs. You could at least find out if the rods are straight, and then see if a shop can fix them. That would save the engine if that's the trouble. There's not anything else that could have reasonably caused that wear pattern, either. It seems probable the motor had water in it, too, so it seems likely that it could have been cranked with some moisture in the cylinder.
This is not the recommended procedure, but worked for me in a pinch to pull the injectors: Just loosen up the retainers a couple turns, until there is a bit of clearance under the nuts. Then crank the engine with the compression release activated. Simultaneously, I stopped cranking and closed the compression release. The injectors, one by one, nicely popped up the little bit to the retainers, and were removable by hand afterward.