-How would you contain the bees while moving them, they have lots of entrances and once I cut down the wall they would be able to get out at the top, bottom and sides also?
If you cut the wall on the outside cavity of the hive, the 2x6 studs will contain them there. The top and bottom, just use a scrape 2x6 nailed in place. If there is a lot of holes in the barn wood, then just use some luan board (underlayment) and attach it to the wall. It's light, will cover all the holes, and will help solidify the wall.
-Colony extends vertically 8' up and down, not sure how to transport it vertically?
I don't see any reason you can't lay the wall section down horizontally in the bed of a pickup truck to take it where ever you need. Or ask the home owner if you can leave it there somewhere and come back after winter to do the cut out.
-Then setting it up becomes a challenge because it would become a big sail, and this is Kansas. I would probably have to find another barn to strap it to.
You could strap it up against a house, garage, tree, etc. Or put it up on blocks horizontally like a TBH.
-Like the idea except for the double work.
May be double the work but you might be able to have a better chance saving the hive.