You don't need to have the secondary (long) chain tensioned to find TDC. You can actually find top dead center with the heads off, using a standard piston stop method as you described previously. But then you'd need to mark it somehow to get back to it later, after you install the heads and valvetrain. Maybe install your harmonic balancer on the crank and make some kind of a temporary pointer to point to TDC when you find it, but that pointer will have to bolt on someplace where the front cover doesn't. Since the harmonic balancer is keyed, you could then remove it, assemble the rest of the components, and put it back on, and if your pointer hasn't moved you should still have top dead center at that position.
I always just install the heads first and then do all the other stuff after that. I made up a piston stop by cutting the center out of an old plug and welding in a steel rod, so I can find TDC with the heads installed. Your dial indicator setup should work just fine too. Also my spring compressor works with the head installed, so I can install checker springs or reinstall valve springs with the head installed. Makes life with the SOHC a lot easier...
Once you get the chain on and tensioned, with the pins in the gears at the zero position, you should be at whatever intake centerline the cams are ground for. You can be off a few degrees, but you should be pretty close to that number. If your LSA is 108, and the cams were ground "straight up" (probably), then you will be at 108 for the intake centerline at that point. From that point you would ADVANCE the cams to get to 105 and 102. TDC gives you a reference point; you will want to check the cams based on this reference point. If you don't have the TDC reference point, you can't know where your cams are degreed.
I think to really get all this you just have to get started on doing it. Wouldn't be a bad idea to consider the first assembly as a trial assembly; don't use any sealer, just bolt everything together, slowly, and start checking stuff until you get the picture of what you are doing.