Daniel,
Expensive, expensive, expensive. It's very time consuming if you want to do a nice job, but not physically all that hard.
I've done the swap both ways on the '94'-95 trucks. Luckily we had a donor truck the same body style so we could get whatever part we needed.
You'll need to swap PCM's and wiring harnesses. The wiring harnesses were different on the trucks I did which involved quite a bit of electrical knowledge to sort out. That was surprising since one was a '94 and one a '95. We didn't expect that many changes in the wiring. Lots of wire tracing and splicing to get the AC and cruise control and a few other gadgets to work properly.
You'll need the heat exchanger and transmission cooler from the auto truck. You'll need the "OD off" button in the dash, you'll need the automatic foot pedals, the steering column, TPS (which requires a different P7100 bracket), driveshaft length changes and a host of other stuff that's not coming to me right now.
If you can find a donor truck, I'd expect about 60 hours worth of labor to swap everything over.
I've actually got a conversion truck in the shop right now. The owner left the clutch pedal and skinny brake pedal in the truck. He also opted to install a rachet shifter to avoid the expense of swapping steering colums.
You definately would save a TON of money if you had another truck to swap with. Lot's of people are looking to get rid of their autos.
You're going to need a strong auto to swap in so choose wisely and ask a LOT of questions to whichever vendor you call. If you damaged that many manual trannies, you'll probably damage an auto or two as well.
Good luck,
Chris