there are four strokes when checking for TDC. Make sure that when the valve comes up its on compression stroke. The Pinter DOES matter, make sure it is straight, and aligns with the crank pulley on the second grove. The marks on chain and gears MUST line up. The marks on the the oil pump and spindle MUST line up. The rotor should be set at number 1 cylinder. its possible to get it 180 degrees out of time, so set it to TDC when the cap is connected, and when you remove it make marks.
When everything is installed, go under the passenger seat (may have to remove seat) the computer has a dial (looks like a screw) and two lights next to it, red and green, spin the dial until the like is just green. If it is still faulty, use a timing light, and see if the Pinter is lining up with the sencond grove on crank pulley. Listen to the beats in the motor, you will know when the rotor is at cylinder 1. make sure that beat is exact to the Pinter on the Crank pulley (Sounds weird but there is a beat to a motor) Last adjust the distributor to advance or decrase timing.
Sorry if this wasnt what you needed
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