Yes,
Observing the spark in relation to TDC is a way of judging timing, however it is not very accurate. I have an automotive timing light that I think will be more precise. I'm just stuck because we are still iced up here in Chicagoland and I don't have an effective test tank.
But I can use a large tub as I did today in the garage. She fires up, but won't run well. ARGGGGG!
Tubs work well actually. Better than muffs as the motor is actually in water.
Whenever I get stumped, I always go back to basics. You said it has good compression, so it's most likely either fuel, air or ignition related.
So what I would do is pick one and eliminate each as you go.
For the fuel, look at the carb, the line as well as the other little things like the filters, pump etc. You said the fuel is fresh, so that's safe to rule out. So check the needles and then reset them to factory recommended settings and then try turning them just a bit to see if that smoothes things out. Again, the shop manual gives you the procedure and it usually gets you 90% there and then you just have to make fine adjustments as the motor is running. But when I set mine, just setting the idle adjustment wrong will cause the motor to not run at all. A turn or so one way and it runs perfectly. You should also observe the fuel bulb as it's running and see if it goes soft, or if pumping it while it's running helps.
For the ignition, the best way to solve those issues is truthfully with a good shop manual and proper tools. A good multimeter can usually sort out those issues, or at least eliminate it from the possible causes of the issues. The back yard mechanic ways often help but sometimes they don't. With a multimeter and a detailed shop manual, it should tell you how to take readings at various points with the mulitimeter to check the various components to make sure they're all good. I realize they're new, but it's not totally uncommon to get faulty parts. The reason I mentioned trying to see if you could observe the spark was because you mentioned that you were worried the plug wires might be backwards. I thought you might be able to see if they were firing in the right sucession without pulling the flywheel back off to check everything. I think from the factory, they used to put a little brass band on one of the leads signifying one of the plugs (top I think). I think the band even said "top" on it. If you changed the wires I gather that's gone though. Silly question, but what would happen if you reversed them? That is assuming they are long enough to reach both.
Let us know if you figure it out.
-Chris