If you use Franks style of wells frame kit, then the center brace triangle also needs to be "removable" where it connects to the side rails. If you weld in the stock piece shown above, then how are you planning to connect it to the side rails? Something to think through...
As for the brat seat and tire clearance, you will have conflict under suspension compression. The flat stock brace that loops up and across allows for the inner fender and outer fender and clearance for the tire. Flat seats are not comfortable for long rides, offer little to no rider support during handling, and create space problems for your tire. All in all, a bad design and a poor modification.
Replacing the flat brace with a hoop solves the structural issue, but you still need to resolve clearance problems. So either the loop closed end needs to be long enough to allow the tire to pass within it, or the shock length needs to be increased, thereby changing some steering geometry. Or, you reduce the wheel diameter changing handling characteristics. Decisions, decisions, decisions.