Well if the only problem is a little bit of contact with the head that seems easily fixable(may require a hammer). The one thing I was not a fan of with the lift kit I did on my old danger ranger was the bolt provided were only grade 5. I would have felt a little better with a set of 8's.
Ya hardware is an issue you have to make a choice of upgrading or not....
I'm a fan of Gr 8 hardware myself and using strictly that level.
Also you will have to deal with clutch MC/SL cyl lines, brake lines, electrical wiring and rad hoses and fan interference along with fuel filler extensions etc,
There is a bit of work to do, though it's all completely manageable.
With my swap, I'm marking the section of the floor pan / fire wall where the head can hit, and I'll mod that accordingly prior to cab swap, along with some clearance mods for the down pipe for the turbo setup. As well, I have to make my electric fan shroud setup prior to my body swap so I can have a solid method of cooling my truck and also I will address my rad hoses too, that about sums up most of my issues!
Other than that...It's all golden
Al