The rotor should be marked in relation to the distributor housing. If that's done, gear position makes absolutely no difference. I can spin the distributor in my big-block Cadillac a full 360 degrees and clock it at any angle I want. The only thing that matters is rotor position relative to the distributor housing. I can even put the plug wires wherever I want so long as I stab it with the rotor close to whichever cylinder is at TDC. After years of working on cars with distributors that were locked to a narrow timing window, that was a eureka moment for me.
That said, you do have a point. If the OP marked the rotor's location in relation to the housing, and then marked the housing relative to the block, the gear position would make it where he wouldn't be able to exactly hit one or the other of the marks.
Check the engine ground just on the lower passenger side of the timing chain. If it's not bolted down, it may be making enough contact to start, then vibrating and stalling your engine out.