Don't worry about the pin.

You stated that you could pump up the brakes with the engine off. You should not have to pump them. It should be tight on the first hit.

It sounds like you still have air in the lines.

Did you bench bleed the MC properly before installation?

I use the little clear hoses that come with aftermarket MCs. The MC gets locked in my bench vise by one of the mounting ears then I take a big phillips head screwdriver that barely fits in the hole and slowly press the piston in until it bottoms. It is allowed to come back VERY slowly and I watch the clear hoses for bubbles. If bubbles get sucked back in towards the port I hold the piston in place and let the bubbles rise to the top of the hoses.
It takes a few minutes to bleed this way but you can be sure the MC is properly bled. The tiniest bit of air will jack with your pressures.