There is certainly an art and science both to breaking in a flat tappet cam.
For this time around though, I think I would just bite the bullet and put a roller camshaft in it. A hydraulic roller will give you a zero maintenance, zero effort on break-in.
If you want to try a flat tappet again here are some pointers:
1. Make sure that all lifters will rotate easily in their bores.
2. Remove the inner valve springs or use break-in rocker arms.
3. Use lots of cam lube on the camshaft and lifters.
4. Use a good break-in
oil, such as Brad Penn or Joe Gibbs.
5. Set the timing and carb so that it fires immediately.
6. Run at 2000-2500 for 30 minutes.
With the loss of the third camshaft, my first advice would be to just put a roller camshaft in it. No worries.