So, I decided that a longtail would be useful for my 12' boat for the Sacramento Delta and all the little sloughs and areas I like to go. I have my shaft housing and shaft complete, and my frame on my motor set up. My question is, what keeps the shaft from moving in and out of the shaft housing? It seems like after I get the U-Joint that the u-joint would be the only thing keeping the shaft from moving. Maybe I'm over-thinking this.

not sure if the name brands have anything different but all the long tails I have built, the u-joint is what held the shaft in place. In addition to the set screws on the key way I put shaft collars in between the u joint and motor, u-joint and shaft housing for added strength.

Yep, still the U-joint, same as last week.... Not trying to be a jerk, it's just that it's completely adequate. Anything additional is just going to add weight and more threads to corrode and deal with when the time comes to service the assembly.
I haven't lost a shaft yet, I've pounded the snot out of 3 longtails for a few years. I haven't noticed it as a big discussion item here because it's just not happening. If you have major vibration, or alignment issues, deal with that if it's causing concern about shafts falling out, don't add bandaids.
You would know if something is coming apart well in advance of getting to the point of a shaft slipping out of a tube especially if you are running seals instead of bushings. I'd be much more concerned about prop removal, seals and bearings and bending shafts than than losing them.

*FULL DISCLOSURE-
*I do not have any financial interest in a company selling longtail props and shafts.