Welcome to the forum
Sounds like you have a good plan and a nice truck to work with. I would definitely just patch the small holes in your floor. If you have never welded, you might check with your local college and see if they have a night/weekend course on welding.
If you want a column shift, that will free up some floor space. Is the column you have is a factory auto trans column? If not, you can retrofit a later model auto column. The '67-'72's look pretty good. Also a column out of a full sized van or mini Motorhome will work well, if you decide to go to the work of switching columns, you might as well go with a tilt also.
Sending you a PM on the dash.