your rear end and tranny will be fine, I've been beating on mine with 4.10 gears and 31" tires and haven't had any issues, been in there for almost a year now, I've even pounded on it in low range 2 wheel drive (hubs unlocked) on the street and no issues...
the cheapest way would be to get pistons, turbo manifold, turbo, vane air flow meter and connector for it along with the turbo computer, it will require the least amount of modifications, I would also suggest a turbo cylinder head (would also require a different intake manifold) to decrease the compression ratio to reduce the chance of knock. what you do is put all of the physical components in place then wire the vane air flow meter into the stock wiring harness along with repinning things to match (a couple wires are different between the '86-88 wiring and your setup).