Hi William. I've been doing some similar work as what you describe. On our Passport 40, we call the area under the cockpit the "Rabbit Hole" as once you enter it, you tend to find more things that you want to look into than you initially thought before you entered it.
Anyway, when we were last on the hard, we had professionals in Anacortes Washington replace all of the sea cocks that did not function. This was and continues to be a relief to me as I know more about those and have a little more trust with them than I do the ones that were left in place. Case point: while replacing the cockpit scupper hoses, I found that one of the ball valves did not properly seal. To my surprise, the hose IDs in this short length of hose had three different sizes and not two. It's tapered from the cabin sole down to the tee (adjoining the lazarette drain) and stepped down once more at the thru-hull. There was a time when a trickle of water was running through the boat as I frantically tried to fit a hose to the fitting in order to get a good seal. I ended up abandoning this approach minutes later by inserting a wooden plug into the fitting. On the positive side, we had a successful bilge pump test that day!
One reason why I mention the store above is that I know these valves are below the water line by about 11" / 27 cm. If you were to attempt pouring vinegar into them, it would need to displace the water from outside your boat. Would this work or would this have no effect? I am not certain of the properties of vinegar vs fresh or salt water. It will certainly be diluted!
While I do not have an answer for some of your questions, I do have an interest in your thread. Thanks for posting. I am looking forward to hearing what others offer as suggestions.
Best regards,
Jeremy
S/V Whale Shadow, Passport 40