I have a 410 with a Waterman 500 pump.
I have a low speed bypass off the barrell valve. High speed bypass off the pump. Main bypass off the pump. Shut off valve between the pump and the final filter before the barrell valve.
When I shut the valve, the engine won't die untill I step on the throttle.
I put a new shut off valve on and the same thing.
I put a three way shut off valve with the return going to the tank by it self and the same thing. any clues?

How long will it idle after you shut off the fuel? Under most conditions, when you shut the fuel off, it won't die right now, it will idle on what is left in the system, between the shutoff, and the nozzles. I like to leave the nozzles wet, so I just kill the ignition, that way when you restart, the nozzles are wet, and haven't had anything dried in them while setting, just the way I do it, everyone has a different proceedure, but I haven't had any nozzles plugged since going this route, running hot laps, and heat race, runs great, sits for an hr, before the feature, and you push off, and got a couple of nozzles plugged, kinda ruins your night. Shut off should be AT the barrel valve, not between the pump and filter. Doesn't sound like you have anything unusual. Bob!

Does this engine have Down Nozzle filters? If so make sure they are not Plugged and are bleeding off as well

After reading your set up again, you need to move the shutoff to the barrel valve, sounds like it's running off of what's in the filter, because the way you have it plumbed, it's still full of fuel, even after you have shut the fuel valve. Bob!

Yes it has down nozzles. I clean the filters every race. I could move the final filter between the pump and the shut off.

It's definitely running on the leftover fuel in the filter after the shutoff. Very few people run a filter on the pressure side. If you have 16 nozzles like me, that also adds more fuel that has to be run out. Both my engines run on for 4 or 5 seconds after shutting off the valve. You don't want to shut off a 360 or 410 engine (any high compression engine) with fuel in the cylinder or dribbling from the nozzles if at all possible. Can't compress fuel... makes it hard to turn over and can bend a rod when it starts. I have also noticed certain barrel valve grinds tend to to this worse than others-even on the same engine.

I was reading thru Kinsler's setup sheet a while back, and unless I read it wrong, which is possible, or they made a misprint, they were now recommending putting the filter before the barrel valve, and not using one before the pump. I run a small one after the pump, but before the fuel valve, no run on with that setup. Still run a large one before the pump, gotta save the pump. Bob!

I replaced the small down nozzle filters with the original long ones and that fixed it.