Do you have pics?
There are some on-line stores that sell rub rail replacements. Below is one link
Replacements carpets seems to seel for about $500ish, but you can also get them made - not sure how much. Also many people have moved away from carpet and used Sea Dek instead.
Gel cracks can be somewhat common, but the causes can be from many things. Cracks around the tower could be from stress or movement/flex of the tower at the mounting points. many people have this, but determining if its cosmetic or structural depends on the severity. some people do their own spider crack repairs. There are lots of youtube vids on this.