Does it matter that the radiator is brand new, maybe 6 months on it.
There are two types of stop leak:
The common, cheap kind is pellets or powder made of aluminum and other stuff. They stop leaks by plugging the hole with a gooey mess that resembles cardboard that's been put in a blender with a cup of water. They not only stop leaks, they also plug the small coolant passages in your radiator and heater core. You may not notice since the radiator has many coolant passages, and some of them stay open. The problem is it's almost impossible to flush out the clogged passages, so when you swap in your new motor and try to drive over a mountain pass in the summer, or go wheeling in sand or mud, your car will overheat because the radiator can only flow half as much coolant as its supposed to be able to. The fact that your radiator is new means it might be slightly less likely to get clogged, since the passages should be pretty clean still, but more importantly, it means that you REALLY don't want it to get clogged and have to buy another one.
The second kind is the liquid glass stuff. I don't think it will clog a radiator, but like I said in my first post, I once pulled a thermostat out of a Ford Escort that was completely blocked off with the stuff, and it had a large chunk of it stuck in the cylinder head as well. It's sort of like epoxy. I don't have as much experience with this style of stop leak as the other kind. I believe it is supposed to actually work on blown headgaskets (The pellet kind really doesn't), and it may be worth a try in your case, but I'd definitely research it more.
The Subaru conditioner has some chunks in it (like the first kind of stop leak) but there is a very small amount of them and they are very small chunks. There is no way it will clog a radiator, and I trust the Subaru engineers to have developed a good product. I run it in my own cars.