Take it apart while it is still in the boat.  You will have to pull the engine, just enough to get the shaft out.  Maybe you got lucky and the damage to the suction is minimal.

Heat the suction with an acetylene torch to get the epoxy to break bond with the aluminum.  Keep the torch moving so you don't create a localized hot spot.  When the epoxy gets soft (will be smoking), you can pry the suction out of the fiberglass.

I try to scrape as much of the epoxy off the fiberglass, while it is still hot and soft, with a wood chisel.

When you go to reset the suction, grind both the hull and suction with 36-grit, to promote adhesion.

The small kit of Poxy Putty is nowhere near enough to bond the suction and blend the transition into the fiberglass.  Get the larger kit.

The transition from the fiberglass hull into the aluminum suction should be transparent to the flow of the water.  While you are blending the transition between the suction and the hull, keep your fingers wet and sculpt the shape as close as you can.  Cured epoxy is difficult to sand under the boat.

I would do the final assembly in the boat.