About the only true way I know of to accurately check for rot is to drill a series of holes in a pattern across the transom. Check the kind of wood that comes out of each hole. That way you can verify the extent of the dry rot, if there is any. Seal each hole with 5200 after you check it. (Use a Q-tip to force the 5200 all the way into the hole). In all cases the very fact you have water intrusion into the transom is cause for concern. If there is no appreciable rot you have to find out where it's coming from and stop it to prevent further damage. Check for flexing again. 6 years is a long time for water to be laying up against the wood without causing any rot. 
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1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
If God didn't have a purpose for us we wouldn't be here, so
Live simply, Love generously, Care deeply, Speak kindly.
(Leave the rest to God) 
Silence, in the face of evil, is itself evil. Not to speak is to speak, not to act is to act. God will not hold us guiltless.
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