Hi Transpac,
Well, that's a tough one to answer without being you, and being there! Never having seen the guts of an Eagle 32, I am at a disadvantage. You say "eww", after opening your fresh water tank and observing a few paint chips in the (presumably) baffled tank you have access to. So what's your tolerance for "eww"??? A "few" paint chips is insignificant unless they're clogging your fixture strainers; only the water quality in your tank really matters.
Have you made a valiant effort to clean and disinfect your tank? If not, buy Peggy Hall's book on sanitation (
https://www.amazon.com/Get-Boat-Odors-Peggie-Hall/dp/1892399156) and follow her instructions exactly on how to bring a water tank to a safe and sanitary condition.
Water test kits for bacterial contamination (NOT test kits for minerals, such as iron, copper or other typical water well contaminants) are available for about $20. You might try one to make sure your water is not simply fouled with sediments or paint residue. Or send a water sample to a municipal water testing lab for professional diagnosis of "eww".
If after you've expended due diligence to clean and sanitize your tank, and are still convinced your tank is unsanitary, then yeah, you will have to access EVERY PART of your tank to clean it completely. And assess the "paint" your OEM applied to the interior of your tank. Not sure why one would paint (and with what) the interior of a fiberglass fresh water tank, but who knows? If the tank was, as I expect, gelcoated at manufacture, the gelcoat may be failing and cracking. IMHO, A pretty tough DIY fix to get it right. You may well need professional assistance at this point.
Regards,
Pete