If both trucks were extended cab short beds, then you could just swap the tanks. You can take the metal sender assembly out of the 98 diesel and put into your 89 tank, remove your fuel filter from the 89 and install the 6.5's lift pump. Your 89 will have the light duty front brakes though(1" thick rotors) where all 6.5l trucks got the 1.25" thick rotors. You can swap the spindles and such over to get the heavier brakes as the 88-91 standard cab light duty brakes were not the greatest, or swap to nbs brakes. The hydro-booster and brake pedal from the 98 should swap right into your 89. You may have to swap the radiator core support over to fit the larger radiator, or you may be able to make yours work with modifications. There was no 34" wide radiator core offered until 90 or 91, so I'm not sure if it will go into yours or not.
If you want AC you will have to have custom AC lines made. Up to 93 GM used sae fittings with R12 refrigerant, 94+ used metric for r134. Being an 89 yours has the early small condenser and the early AC control system with no manually selectable recirc mode. You can change the condenser, but your trouble comes in at the evap. The 98 hoses will only work with the 96+ accumulator, and the 96+ accumulator will not work with your 89 evap because of the thread change. You could pull the dash out and swap to the 94+ evap, but as far as I know it will not fit in the early evap housing(r134 evaps are thicker), and I don't believe your 89 control head will work correctly with a 98 evap housing(the doors changed iirc). So it's custom AC lines only.
Wiring is where things get tricky. You will essentially have to turn the 6.5l engine harness into a stand alone. The speedo should be able to work by running your transfer case speed sensor signal to both the cluster and the VSSB. 89 has the moonie gauges that have a built in DRAC in the cluster, the 6.5l has to have a VSSB to read the speed sensor and provide the neccesary speed signals.
You will have to do some work to make the 89's mechanical shift linkage work with the 4l80e trans. 98 used a cable shifter, so you will have to change the shift arm, most likely have to change the 4l80e's long shift shaft to a short one, and lengthen the shift rod. You can drill new holes in the 89's frame to move the trans crossmember back.
These are the major details that come to my mind at the moment, but I'm sure I'm overlooking quite a few. It's a doable project, but will be alot of work for all of the small details.
Maybe even make a build thread with lots of photos as you go along. we all can give you some good pointers. as for the drive line and trans. I don't know how stout a 700R4 is, but if you want the overdrive and TCC lockup and don't want to hassle too much with the electronics side of things, that trans might be an option while converting the engine to mechanical injection with a db2 pump. those can still be has 100% new and on the plus side of things with diesel prices the db2 can handle WMO and other darker colored diesel fuel without any issues. the ds4 on the other hand can't run black diesel and doesn't like red diesel due to the optic sensor in the IP.