I think is time to take it apart.
You got problems. The only way for you to know how serious the problem is to take the headliner down. I have a 34' that I will be selling soon and I don't have that soft feeeling when I walk on the deck. You can patch it by injecting epoxy into the void holes of the deck. Reinforce it with firbeglass. Buy a book how to do fiberglass. When I started on my 46' I bought several books. If the deck is wet you might have to tarp it and dry it. When I bought my 34 it had stress cracks on the deck. I epoxy the void holes and I used the boat now for 10 years and no problem. If your deck is wet, you need to get it dry. If you are flexing is because something has giving up in your structure frame. Dry-Dry Dry-Epoxy and epoxy again. I am also building a new rudder for my 46'. I just took the old one apart and duplicated the whole thing out of foam and fiberglass. Get into the internet and do some homework. By the way my 46' was a sunk and giving up for total lost boat. 800 hours later and about $30,000 on material it starting to look like the $450,000 boat it was. You have a $30,000 to $35,000 boat in your hands, use your time wisely. Cost can get out of hand when you are dealing with a low priced boat. I also looked at several hurricane boats for sale. Most of them you can't get your money back on them. Try a 46' hunter for $15,000 with a 60k repair bill is not a good deal. A 46' Swan for $20,000 that is worth 400k give you lots of room for repairs. I hope this helps.