The default firmware is set up for acceleration, jerk, and feed rate appropriate to the thread rods. When you go to Acme rods, they can be changed to make things work faster. There is no problem with leaving them on the "slow" settings. The Z axis never needs to move very fast with normal printing.

If your head is crashing into the bed, that has nothing to do with the screws. The crash is controlled by your Z axis limit switch.

Calibrating the steps / mm is fairly straightforward: Tell it to move 100 mm and measure how far it moved. If it moved 50 mm, your steps / mm number is too small. (you told it it would take 100 steps and it really needs 200). If it moved 200 mm, your steps / mm number is to large.

Bob