Patience is the key! Measure loads and offer them up in various ways - depending on type you need to check they clear the transom and tubes when up, down and being moved. Also check the wheels in place with the engine fitted and that you have full arc of movement without fouling anything.
Use SS fittings throughout - when drilling transom drill a small pilot hole then drill outside in to the middle from each side to avoid any breakout of the ply.
Seal holes with a decent marine type sealent. Use SS spreader/'penny' washers on fittings.
Launch wheels suitability
It is unlikely you will have enough height to use them with the engine down - not an issue though.