First, welcome to the Forum, I hope someone can help you get a resolution to this.
A few questions:
1. What was your original 88 Cobra OMC model number?
These should be your options:
574AMLGDP ,
574APRGDP ,
574APRGDP, 574BMLGDP, 574BPRGDP (unless you put in a different motor size)
This tells all of us what your original setup was.
The 57 is your motor in Liters 5.7L
The 4 is your carb (4-barrel)
A or B is First or Second model release
M or P is Steering (manual or power)
L or R **this is the important one for your posted question** (Left hand or Right hand Propeller Rotation)
GD should be your 1988 year
P is Model Revision
2. By any chance did you install a new or different prop when you put the boat back together?
As noted above there are LEFT HAND props and Right HAND props. (This would be an easy fix/swap!)
3. What is your propeller part number?
The part number should be cast or stamped into the prop. (my two props are OMC and the number is cast into the face of the exhaust (hub) of the prop)
Maybe we can find if this is a backwards prop for your setup.
4. Was the new motor built back to original spec, or was is modified?
5. Is the motor a car/truck motor or marine motor or OMC motor? (or give us as many details as you know).
6. Did you also change out the stern drive or rebuilt the outdrive?
Hopefully this will give the group some information to start helping you with.
Hopefully this is just a backwards prop or else you will be in for some big changes.
Best of luck,
Offrddrver