I am in the process of replacing my transom and I was wondering if I should use something to bed the wood to the aluminum? If so, any suggestions on what to use?
No need to do that, it'll just be something else to remove the next time it needs replacing.
It would be a good idea to put an aluminum primer coat or 2 of paint on the inside of the transom where the wood will be touching the aluminum to prevent galvanic corrosion.
I haven't seen any type of barrier between the wood and the transom aluminum in the boats I have had. Just coat the wood good with spar urethane or an epoxy (3+ coats) on both sides. Also recommended is to drill the bolt holes a little oversize and coat the insides of the holes with your preferred coating.
I just replaced mine. I may have gone overkill, but it should outlast the aluminum. I used 2 layers of 3/4 ply with epoxy and a layer of fiberglass matt between. I covered the all outside surfaces with epoxy and 'glass cloth then overdrilled the mounting holes and filled with thickened epoxy. I redrilled the holes. A coat of paint and install with 4200 for the screw holes. No chance of rot again...at least for a long time.
-J