1) You current gearbox is probably repairable fairly cheap unless the gears or housing is trashed. You can get the bearings and seals much cheaper at your local bearing supply than from MCI. If the shaft is grooved where the seal goes either reposition the seal or use a speedy-sleeve to repair it.
2) If your gearbox is trashed, get with BK and make a deal on the parts that he has.
3) If BKs gear box won't work then one like this might work. http://www.surpluscenter.com/New-Arrivals/1-1-32-HP-RA-GEARBOX-3-SHAFTS-ALL-KEYED-13-1423-3K.axd
4) If you want to re-engineer the entire cooling system then go ahead but the folks at MCI and Detroit Diesel did it for you many years ago. Make sure that the water pump and thermostats are working properly. Make sure that your radiators are in good shape and that the seals around the radiators and panel doors are in good condition. The fans must pull outside air through the radiators. If there are leaks around the radiators or the blower compartment then the fans will not suck enough air through the radiators. If you want electric fans make sure that they are 100% duty cycle. Fans from a car are not meant to run all of the time and will wear out quickly. I hydraulic motor/fan will require a separate pump, reservoir, and hyd oil cooler. The hyd setup will probably use more horsepower than the belt driven fan did.