Travis why do you want to get rid of the auto? A well built auto is a very nice thing.
By the time you buy a good six speed $2,500 - 4,000 good clutch and pp $1500-2000 and have it installed clutch r&r is about 8 hours, apply your local shop rate plus the conversion time you could have your auto trans built to the hilt. And not have a butchered truck.
If your going to do a conversion correctly you need a new dash panel, cup holders no worky with stick. You also need a steering column to get rid of the gear selector along with a new gauge pod, no need for a gear indicator. Not sure what kind of mounts/cross member set up you might need, the older trucks you could just move the original member back a little. And whatever it gonna take electrically to not set DTCs all the time.
Not saying it can't or shouldn't be done, just do it properly.