Once you slide the pump assembly in place, check the drive shaft hole for alignment. Basically, I use the front bolts to adjust side to side and the rear bolts shim to center up/down.
First, put the front bolts in place but loose. Check the drive shaft hole for side to side alignment. If you need to adjust, use a punch and insert it into one of the rear bolt holes and use it to leverage the pump assembly right or left, then tighten the front bolts to hold the correct position.
Now check for alignment up/down. If adjustment, needs to be done (usually the drive shaft is too low in the hole), add shims between the hull and pump mounting brackets at the rear pump bolt holes to lift the drive shaft.
off alignment:
Aligned:
Now clean up the mid shaft surface area and add marine sealant, chalk or silicone sealant to the mount spot in a circular fashion.
Mount the mid shaft in place. Its a also a good time to install the bilge since it is located under the mid shaft and the motor install will make it difficult to install later. Notice the ADA coupler has a hole in the center, unlike the yamaha coupler which is solid and caps water coming in from the spine/ shaft area. I siliconed my shut.
Before installing the motor, you will need to bolt in place the motor mounts on the carb side. The bolts are too long to be inserted with the intake manifold. Therefore, before you mount the motor adapter plate, put in place the bolts and finger tighten the mounts (do not torque them down yet)