Re: Drilling Transom Bracket Holes...
I have two suggestions:
1) To drill perpendicular to the transome, take a good piece of 2x4 and drill the size hole you need using a drill press. Then hold the 2x4 against the transom and use it as a guide to keep the bit "square" to the transom. If you need to drill at an angle other than 90*, then set the drill press at the appropriate angle when drilling the guide hole in the 2x4.
2) Transom rot often starts where bracket bolts pass through and the sealer (if any was used) fails and water starts leaking in. To prevent this in the future, drill oversize holes and fill with epoxy. When fully cured, then drill the actual size hole through the epoxy. IE drill a 1" hole, fill with epoxy, then drill the 5/8" hole for the bolts through the 1" epoxy "plug". Now, even if water does get past your bolt hole sealer, it will not get into the wood of your transom.
Best of luck with the boat!