Hey Stone, welcome!!!
Your splashwell will provide some all important structure to your rig. She'll be a floppy noodle without it. Danger! If you take it out you'll need to some how provide structure to keep your hull from collapsing.
If you take a gander at any 12/14/16 foot utility boat you'll see benches running from one side to the other. Kinda sorta like the backbone of the boat, holding things together. You'd pretty much have to do something like that to keep the rig from folding up on ya.
Head on over to the Starcraft section on your transom corner. There is a fella there that can give you a hand
Your rubrail trim will be a little more challenging. Looks to me like a bear chewed off about a 3 foot section there, bummer. I'd say you have two options on that. 1. Find a guy who is scrapping out his old Starcraft, grab a small section of his rubrail trim, and scab it in. 2. Pull it all off and start over with a new rubrail and insert from a place like Taco. The first option is a needle in a haystack and the second is just a bit pricey.
Welcome to iboats, glad you are here!!
Edit: Actually, I just posted to MD's 93' Starcraft project and his is a good example of a rig with no splashwell. BUT, you can see that big ol bench in the stern there. You'd pretty much need to go to something like that if you don't want the splashwell. If you don't like the big bench, I'd say keep what ya got, eh!