In reality there's not a whole lot to think about versus a gas version truck when contemplating mods.  The only things I can think of is: 1) If your engine puts out excessive torque, you need to take this into consideration and eliminate weak points.  This can be tremendously expensive and troublesome.  2) The added weight of diesel engines means you need to compensate for them elsewhere.  This means added suspension capabilities particularly up front, and elsewhere.  And: 3) Diesels and gearing.

Diesels and Gearing:
This is addressed elsewhere in the site particularly in the Cummins conversion transmission section and in the crawlbox section but I'll say it again.  Because diesels sometimes have lower rpm limits you need to take extra caution in figuring out your gearing.  For an off-road only vehicle lower is better in almost all situations.  For an all around use vehicle you need to be smarter.  If you have trouble figuring out what to do email me and I'll type up a thorough response and post it here.

Secondly, particularly with naturally aspirated and low output diesels, you need to pay close attention to gearing, particularly when putting on larger tires and messing with lift.  The general ratio is this:

On any HJ60 or BJ60: They come with factory 3.73 axles gearing.  This is fine for low altitude and flat only areas.  But I would recommend immediately going to 4.11s even with stock tires.

You might want to check out this page on axle gearing in general.