Brake pedal sits too low

To clarify, the OP must be talking about a manual MC.

As I recall, in the photo of post #4, you should remove the piston retaining tab and attach the dust boot to those 2 holes, while holding the piston in (its return spring tries to push it out). The dust boot has a metal plate which keeps the piston from coming out. Most manual MC's come w/ both a dust boot and pedal rod (see rockauto). Yes, you can buy the rubber bushing for the end of the pedal rod by itself. I did so when I ruined one from a test fit (before I put the boot on). Might have bought on ebay.

Always remove the brake light switch (or slide way back) when doing this. You don't want the pedal to bottom out on the switch. The MC should push the pedal back. Once assembled, then slide the switch forward so the contacts open when the pedal is at resting height, and should be slight free motion left in the switch (i.e. not bottomed out). If not, the MC piston may not fully retract to expose the refill port, and thus not work, which is a common issue discussed here.