Can I put manual 3.0 ranger motor in a 89 3.0 auto ranger?

You have to remember that engines with manual transmissions have a flywheel as opposed to engines for automatics having a flex plate that the torque converter bolts to

Was just wondering if flex plate will bolt to auto crank

It should, but I can't say for sure. I do know that when looking up replacement crankshafts there's no distinction between manual or automatic so the bolt holes in the back of the crank should fit both.

not great on fords, chevy guy, this crank has a protrusion with the pilot bearing in it, worried the converter going to hit it

There are a lot of Ford forums and probably some dedicated to the Ranger and those members should give the most accurate answers.