Wow that's a lot of money. I'm going to be putting my 93 second gen with 2.8 diesel up for sale next month (the whole truck) for $6500 Canadian, so you can imagine it sounds high to me for just the engine.... If you want new, then obviously that's the way to go, but I regularly see whole/running diesel Pajeros on Canadian sites for about what you're being quoted for just the engine. Even if you just buy one for parts, at least you have everything you need, diffs, trans, etc. Maybe you've looked at this already and simply want a new engine? That's cool too.

As far as diff ratios, my 4D56 came with 488s and I feel that with any shallower it would've been under geared. I ran 33s on it, but still... My current Pajero with the 2800 diesel has 490s, and again, I wouldn't have wanted any (numerically) lower than that.

I'd definitely recommend an intercooler whichever way you go, and an EGT gauge. These little diesels will pull all day, but to their destruction if you don't manage the heat.

Not sure if any of this is helpful and you know what opinions are like, but enjoy your project!