There are multiple options - depending on budget, timeline, etc.. My friend Ron SanGiovanni (Ronnie Roadster) builds flatheads and really knows his stuff - he is in CT.
Another option is to put the engine on a pallet, take it to Fastenal and send it to Fowler Performance in Columbus Ohio (they do all my machine work). I highly recommend the work of both Ronnie and Jeff . . . they know what they're doing, have the right equipment and are very versed in all things flathead. Ronnie races vintage flatheads at Bonneville - so if you are wanting a very high-performance flathead, he can design the exact combo you want. Fowler would be great for stock to 3/4 style street performance builds . . . so it kind of depends on what you're looking for and how much you want to spend.
Feel free to PM me for any more information . . . am very versed in all "styles" of flathead engine builds.