about that 5200, it's a great product that will hold pretty much forever and it does have it's uses but you would be much better off using sikaflex 241 or 3M 101 to re-bed any deck hardware. The reason for this is that sooner or later you will probably want to actually remove some of the items that you have re-bedded. 5200 is entirely too tenacious for this and you will most likely end up tearing up some fiberglass upon removal. NEVER bed wood down with 5200 if there is any chance you will want to remove that piece later(in one piece, that is). In my opinion, 5200 is overused, even 4200 is too strong for most applications and any boat that has had everything bedded with 5200 is a complete nuisance.
As for your engine controls, any bulkhead mounted shift/throttle arrangement will do. inboard controls are pretty standard, they all use teleflex style shift and throttle cables. Take a look through the west catalog, or cruise ebay for a used one. Morse is a great, well trusted brand, but others work fine as well.
A note on the atomic four. There is nothing wrong with dropping another one in your boat, but seeing as you don't have one yet, perhaps you should also be looking for a small diesel. Universal made one that dropped right over the old atomic four engine mounts, others may need some modification to the engine beds. It's a bit more work, but you must consider that seeing as the old engine has already been removed, a lot of the work has already been done, so if you have the means to repower with diesel, now would be the time to do it.
Finally, a comment on the transom/outboard combo. Purely academic at this point, but when considering mounting any outboard on a transom, it all comes down to the bracket, it's location, and how firmly it is mounted. Others have expressed deep worries about hanging a 30hp on the transom of your boat. Before getting too worked up about it, one must consider that the sternpost and transom have been built to carry the load of the backstay, which, under way in a sea, produces much larger stresses than the weight or thrust of a 30hp outboard. The key, of course, would be to hang it properly. w\Which means using a strong, "gill bracket" type mount for the engine, properly mounted with sufficient backing plates, preferably on centerline, stradling the sternpost, etc. All that being said, despite it's usefulness, I tend to think any outboard bolted on the back of a bristol 29 as somewhat of an abomination. A "hack" solution, if you will. Granted, their is something to be said for the economy and "quick fix" aspects of that route, and sailing with an outboard off the transom is much preferred to a boat on the mooring or still on the hard with a dead or nonexistent inboard. Just not something I would want to consider properly fixed, but rather a temporary solution.