I cannot offer any first-hand advice about removing rotted wood embedded in the transom of a Boston Whaler boat, because actually I have never performed that repair.
In this case the extent of the rot is not yet determined or explained. If the rot is confined to near the holes used for the lag screws used for the lower engine mounting holes, you may be able to remove just the rotted wood in that area by working through the existing hole in the transom. A product called GIT-ROT is often mentioned; I have no experience with it. More at
https://www.boatlife.com/boatlife-blog/ ... e-git-rot/If there is extensive rot of all the wood in the transom, a complete tear-off of all the wood may be needed. Search the archive for articles on this topic. For example:
Go to BING.COM
Enter this as the search argument:
site:continuouswave.com repair rotted wood in transom
The 3,900 results will provide a lot of reading
Here is the URL for that search:
LINKRegarding the methods for properly mounting a BIA transom mounting bracket to a boat with a shallow engine splash well, there already are several articles on precisely that topic. See
Transom Mounting Hole Layout for Shallow Splash Wellhttps://continuouswave.com/forum/viewto ... f=7&t=5808See the FAQ at
Q8: How Does the Engine Mount to the Transom?https://continuouswave.com/whaler/reference/FAQ/#Q8The use of lag screws is really not the cause of the problem. More likely the absence of proper sealant is the cause.