As far as the transmission, they used to make an adaptor to mate a Flathead Fordomatic to a Y-block, but that was decades ago.
The flathead power steering pump brackets are different from the y-block ones but You may be able to buy the top cast iron water-pump bracket and bolt new from repro parts suppliers. Not sure if the flathead adjustable pump bracket will work on a Y-block water pump bracket. There is also a rear stabilizing pump bracket that bolts to the first bolt-hole on the Y-block exhaust manifold. If they don't still sell that new, you can fabricate that if need be. It also has slotted hole adjustment that may be difficult to duplicate without a pattern from an original one.