mossyz,
Your plumbing idea, of having two bypass circuits coming directly off the C3 thermostat, will work just fine. As you suggest, it doesn't matter where the valves are in each circuit (beginning, end, middle) it will reduce or cut flow in that circuit so the flow will increase in other circuits.
As I mentioned in a previous post, but I didn't elaborate much, another option is to plumb the selkirk heat exchanger on your open-thermostat, radiator circuit rather than on the bypass circuit. While this is not the selkirk-recommended installation, it seems logical to at least experiment with it. In the end, it made more sense to me and seems to work better for me on my 2020 YZ450F. When I was trying to get engine temps higher, I saw little reason to have the Selkirk heat exchanger on my bypass circuit and pulling heat out of the engine when I was trying to get engine temps higher. I only wanted active heat exchange when my engine needed to be cooled, so when my engine's thermostat opened. Since the C3 thermostat has an internal bypass, you'll always be pushing some coolant through your radiators (and heat exchanger the way I plumbed it) so no risk of cold shocking your engine. When my bike is warming up at the trailhead, well before the thermostat opens, if you put your hand on the radiators or selkirk head exchanger, they are warm since that small amount of coolant is always flowing through them. Once the thermostat opens, then a lot more runs through that circuit and cools the engine right down and thermostat closes again.
I keep my radiators uncovered on trail and covered when off trail. If there isn't a lot of powder, then I often leave radiators uncovered off trail, too. Temps off trail have mostly been staying 175 - 185 degrees F (I have a 194 degree F thermostat). Some super light powder days I might be down to 165 F. Way better than the 140 degrees it was running with the Selkirk plumbed on the bypass circuit. Plus, my engine doesn't cool off as fast when I stop for 5 minutes to talk and then start it back up. Was dropping to 120 degrees super fast (during a 5 minute stop) before I replumbed because heat exchanger sits in the deep snow cooling off and, when plumbed on the bypass, all that goes into the engine as soon as you start up. Some Yamaha owners have put spacers between the heat exchanger and lower surround so it cools off the engine less. I want the heat exchanger to remove as much heat as possible, but only when heat removal is needed, hence why I plumbed it on the radiator circuit. I love it plumbed this way and it works better for my particular bike and setup.
On the Yamahas, the radiators are plumbed in parallel and not series. The easiest place to add the heat exchanger to the circuit was in the lower radiator hose coming out of the right radiator. I was leaning towards it being on it's own circuit and receiving coolant before the radiators, but that complicated plumbing and valves/splits and, at that point, it was going to be a temporary experiment and first hand fact finding, but now I'm leaving it.
So my flow is as follows: A single bypass circuit out of the C3 thermostat goes only to C3 heated bars then back into the C3-provided lower radiator collector hose. My thermostat-on circuit flows to the top of the right radiator (like stock). Left Radiator plumbing is stock. For right radiator, the outbound hose coming out of the bottom, I put an inline adapter to reduce to the selkirk hose size, then it runs to the heat exchanger, comes back through another inline hose size addapter, then to stock hose size and into the stock metal Y collector. I originally did this just to experiment, but it works so wall, I'm leaving it.
Many ways to plumb these and have them work well. This was just the way that worked best for my bike, snow conditions, etc.
