Yeah - get on the boat with the CONEX boxes and enjoy the ride. Ugh. Just following orders - follow the load until it's signed for.
USAF/SOCOM, 6/1989-6/1995. Home-stationed here in CA (grew up in IN.) At least you won't have to listen to your kids - too bad your wife doesn't travel well (mine does! :kissyou: )
1) The "internal" tranny cooler is the one that's already in the radiator - if you follow the lines up from the transmission to the radiator, you'll follow them right into the cooler. It's a hollow cylinder in the radiator tank.
They put it there both to cool the fluid (from about 230* to about 210*) and to heat it to operating temperature quicker (from ambient to 190* or more.) You aren't going to harm anything by taking the internal cooler out of the circuit and going with the external unit only - and you'll be able to cool your transmission off more. If you were going to tow regularly, I'd highly suggest a transmission fuild temperature gage, and take the temperature before the fluid gets to the cooler, not after. (Ideally you want both - that will tell you if the cooler's clogged. But, pre-cooler temperatures are closer to actual operating temperatures, and spikes in temperature are pretty reliable indicators of problems. Since you're driving the Al-Can, install the gage. It can get lonely out there...)
4) The fan clutch is actually a viscous coupling that is thermally activated (uses a really thick fluid that is supposed to get thicker with heat.) This fluid has a shortish service life - say, five years or so. I tend to write the date I replaced mine on the body of the new cooler to help me keep track (four XJ's.)
The idea of "pinning" the fan clutch is to make the fan "always on" - the fan clutch is a variable coupling, and it never reaches 100% power transmission (I think it peaks around 80%.) You want to use two or three bolts for balance, to reduce stress on the bearing behind the fan. If you don't know how to set up a hole pattern, a machinist on base (check the aero shops) can do it for you in about 15 minutes - show him my first post and he should get the idea. This will keep the "string-driven thing" on all the time, which will help both your engine temperatures and your transmission temperatures (the tranny cooler mounts on front of the radiator, and uses the same fans.)
Most people who hear about "going solid" at the fan clutch fear some great power loss, but it's a non-issue for engines like ours in street vehicles or off-road vehicles - and I'd sooner have a solid mechanical primary fan than an electrical off-road. There's no real useful reason I can think of for going with electric fans only in our applications - I save that for racing vehicles (I might do it with Project: REDSHIFT, but I haven't decided yet.)
With the 99, you should have the dual diaphragm booster, which will give you better brakes. Check your brakes a month before you go - if the look a little worn, change them then! There's a "break-in" cycle for brakes - heat them up too much too soon, and they're history. Not the sort of thing you want to have happen with a trailer... You're also due for a fluid change - or at least a thorough bleeding - but you'll have to check your user manual for that (I haven't gotten an XJ w/ABS - yet.)
If you have any more questions, feel free to ask! We do what we can...
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