I have done everything from washer replacement, ss plug whole replacement(nice), flapper replacement on side scuppers to ball/cage type (my favorite), side scuppers sealed and modified to transom scuppers/ball in cage. I prefer the side scuppers with ball in cage if anyone is pondering the modification, they are more effective at draining everything out and just as dry as transome without the loss of transome storage area.
Lets see, I did diagnose backsiphoning and thought that was the end all to end all fixes but was a side effect of water intrusion into inner hull, causing the transome to sit @1-2" lower at the dock and that caused the bilge thru hull to sit just under the waterline which allowed water to run back into the bilge after the bilge completed it's cycle.
So, I am back to trying to make sure there is no continuous inner hull water intrusion which could cause the "other" water intrusion situations.
Check all your hoses and clamps and the thru hull nipples for cracks. Check baitwell pump for cracks or leakage.
Use a water hose while the boat is on the trailer and see if water leaks out of the transom plugs....mine never would but should be easy to check.
My next diagnostic method will be selectively plugging thru hulls with dowels to isolate a potental leak. Gives me something to look forward to in the Spring.
I'd do it now, but in Alabama, the waterlevel in the lakes are so low from draught I can't even launch the boat at the local lake! That lake has a leak too!
Guess we will eventually run out of ways for water to enter a boat. All boats leak for the most part at some time but the drier the better.