You have a strong running Engine, and a much more heat to dissipate than what was in it before, and cooling it for off-road use is going to be a challenge; be happy you don't have an Automatic then you would have even a bigger problem.
Yes new engines will run a little warmer during break in, but not enough to cause much of a problem if everything else is right, by 500-1000 miles it should stabilize.
Your Fan and Fan Clutch sound like a good place to start to me. If you haven't ordered already check the specs on components on a 1 ton truck from 87-95 era, that is just my advice.
Placement of the Fan within the shroud is critical, the gap between the outside of the fan and the shroud should be minimal, but you must allow for the engine flexing in the mounts, so I would shoot for 3/4 inch clearance. The blades should be half to 2/3 thirds covered by the shroud, you can get a little more cooling by the use of spacers to adjust this dimension.
There are so many other variables, some Aluminum Radiators are designed for High Volume Water Pumps, and sometimes High Volume Water Pumps are part of the problem, is your water pump pulley 1:1 ? Or is it a higher numeric ratio ? Is your Timing retarded ? If you engine comes on strong is probably OK, but it would be nice to know the advance curve. It might be worth you trouble to have the Radiator tested for the presence of Hydro-Carbons, to eliminate bad head, block, gasket problems. Any good shop should be able to do this very inexpensively. Do you know for certain your Thermostat is working correctly ? Are you getting enough flow thru your Radiator ? There is a great thread in the 60s FAQ section on overheating that covers the problems you might have. Just because parts are new, doesn't always mean that they work properly, or that you were sold the part you ask for.
And Elbert gave you some great advice, my only difference with it is saying for certain it will work, instead of it may work, being your setup is quite different from his.
One last thing - ask Blueprint Engines for their advice, they should very knowledgeable professionals who work with problems like this day in and day out.
All the best !