Here is a six year old thread on the subject.http://www.jalopyjournal.com/forum/showthread.php?t=187851&highlight=flathead+water+pump At the time they came out good quality waterpumps for flatheads were hard to find and not the greatest quality while you can get new ones today that are pretty decent and the 409 pumps are fairly hard to find. I think the main advantage in some installations might be the simpler belt arrangement.
I believe you have nailed the main reason that the 409 pump conversion was dreamed up,,the availability of quality made and redesigned Flathead water pumps is a better way to go today. HRP
Go to this site and look at the pictures of Cotton Werksman's T roadster, http://www.macsmotorcitygarage.com/2013/07/07/american-legends-at-the-gilmore/ This is about the best set up for the 409 water pump conversion because it sets the fan down low on a short radiator. I had the conversion on my '36 Ford truck and it positioned the fan too low and I had to run an auxiliary electric fan on the upper part of the radiator. I wound up going to the '48 style fan with stock water pumps (Speedway's) and now it runs all day long 180 degrees with 180 thermostats. I'm keeping the 409 conversion for if I ever get a wild hair and build a modified.
I started producing a 348/409 conversion kit about 15 years ago and it worked very successfully. I sold a bunch of them and still sell several a year. One of the draw backs for a builder using an early motor was converting to the late style distributor. I addressed all this with parts available. On several installs I raised the fan by using a truck pump, not the best looking but it worked. I originally started doing this because there was not a really good way to put air on a FH so we designed brackets to make this possible. Now there are several options for FH air. I'm doing another ch***is that will use a French block with my 409 kit, a Roadrunner blower and 5 speed. Gary at Cornhusker
I have 18,000 miles on my truck with a 409 pump, with no issues at all, and my flathead is far from stock. It was almost 100 degrees at the Syracuse Nationals on Friday and I idled around in 1st gear for almost an hour an never went over 200, stayed about 190 most of the time. On the freeways I never go over 170. And as for the pumps, many people sell them, including Edelbrock. If you have any questions, shoot me a PM. Eric