Tried to set timing, can't seem to get it to work

I have a 1985 chevy c10 truck, which had a 305 engine and I put a new 350 engine in it. I am still using the harmonic balancer from the 305. Since I've been told that the timing mark on the 305 will not work, I used a piston stop to turn the engine on the compression stroke until it stopped, made a mark, turned it the other way until it stopped and made another mark, then split the difference and put a new mark on the harmonic balancer, which was about an inch off from the original mark on the balancer. On the 305, the timing plate was welded to the middle of the timing chain cover, but on the 350 the timing mark is on the side, held in place by two bolts on the timing chain cover next to the power steering pump. I had the valve cover off when using the piston stop so that I could see the intake valve open, to be sure that I was on the power stroke. Then, when the new mark was lined up with the zero mark on the plate, I dropped the distributor in with the rotor pointing at cylinder number one (I am sure it was #1, it was marked on the intake manifold). I managed to get the engine running and put the timing light on spark plug wire #1 and pointed the light at the balancer and the timing mark was nowhere to be seen. This has happened to me before on other chevy small blocks. It doesn't make any sense to me, if the timing mark is at zero, when the #1 wire fires, then the light should flash at the right time and I should see the mark, but I don't. I also blocked off the vacuum advance to the distributor, so the vacuum is not throwing it off. The truck runs, but not as well as it should and I can hear the engine missing sporadically. I put in a new dist, coil, wires, and plugs so it should not be any of those causing the problem. I think the problem is the timing, possibly it is something else, however if I can't get the engine to flash on cylinder number 1 like it is supposed to then at the very least I cannot eliminate timing as the problem. Later on, I took the distributor out and put it back in. The rotor was not pointing at cylinder #1, but it was pointing at the wire for spark plug number one. Anyway, it can't be too far off because it runs pretty well that way. After all, as long as the #1 spark plug fires at TDC for cylinder #1, as far as I know it does not matter if the rotor is pointing at cylinder #1 and it didn't work any better when it was pointing at cylinder #1. Just out of curiosity, I moved the timing light from wire #1 to all the other ones, just to see if the mark lined up at one of them but it did not.