If the mark at one end(pulley) lines up but the other end(flywheel) doesn't this is the first thing that needs sorting, something is wrong possibly a mismatch of components.
Use a dial gauge to check the true TDC, then work from that to determine which is wrong, don't forget BOTH valves will be closed on number 1 at tdc.
If the flywheel is out everything to do with ignition will be out as well.
tabetha