Ok, 2001 Ford F250 with the 7.3 engine. 363,000 miles.
I knew something was going to get me and it turned out to be the tranny. Theses trucks are notorious for transmission problems.
The question is, how much, on average, will a transmission repair cost? The truck is only worth about $6000. Am I totalled?
What exactly is the problem? Automatic or manual? If you don't know the cause, what are the symptoms? Leaks? Slipping? Uneven or clunky shifting? Does it still drive? Have the engine and trans already been rebuilt?
The answer depends on the extent of the damage to the transmission. IIRC, the transmission seals are a common problem on those trucks. If you've been running the trans dry, you'll probably need a new gearbox, meaning you're totaled. If the problem is limited to some leaks and slipping on an automatic, you might be able to justify to cost of getting the seal and torque converter replaced.
Regardless, I'd prepare yourself to discover you need a new vehicle. As saverem said, you're sitting at the edge of a money pit. If you can sell it for that $6k as it sits, I'd go for it and use it as a down payment to get yourself into another good 2000-2006 truck.