This was, in a way, how I got my start. All my horses started with bad, overgrown, flared feet in the beginning, and I went through several local farriers and never found one I wasn't "fixing" their work after they left. This is also what Amarea is going through right now with her mare Rain in transitioning to barefoot.
You don't want to try to measure for boots with the feet in bad shape. Get the shoes pulled (pay a farrier to JUST come and pull shoes if you have to) and trim your horse down, removing flares as best you can for the time being. Transitioning to barefoot is NOT an instant thing, it can take time and need quite a bit of support from you. Plan on once a week or every two weeks trim schedule of your horse for the near future, to get his feet back in shape, and expect it to take a while for healthy feet to grow to the ground - it can take 6 months to even as long as a year, depending on how bad of shape they are in.
Don't assume you can buy one pair of boots and stick with them. Chances are you will need to get him boots that fit him for now, and lower sizes as the flaring grows out and the fit changes. Amarea has found an easy boot trading group, where people trade used boots amongst each other. I'll ask her to come on this thread and give you the details.
There are some VERY educated members on this forum that can offer some tips and help you out along the way, I was lucky to have someone giving me some tips from the beginning.
Good luck with it and feel free to pm me with questions, I've not been doing it long, and there are certainly more experienced members on the forums here than I am. But I now trim the feet on all the 9 horses in my care, and have seen a LOT of improvement.