After owning a shuttlecraft jetsport for quite a few years, I can tell you there is no manual that will give you that information.
Your only option for factory components would be through their website. Keep in mind that they were bought out by a company in Australia that is doing what they can to provide new boats and parts.
That being said, Jetsports are no longer in production, and shipping from Australia is horrible!!
The good news is that the bimini top is nothing you can't buy from Overtons, west marine etc. Just get dimensions and order the color you like. Mine was factory, and there was nothing special about it other than the color matched the graphics.
Your best bet on a custom cover is to go to your local tarp repair shop, or cover maker local to you with the boat. They will literally throw the bolt of fabric over the boat and custom make you a cover with as heavy of fabric as you want, and with what features/colors you want. Many times these can be the same price or less than if you had ordered it new with the boat.
There are also many custom upholstery shops that can recover your seats. Do some searching online for those that have recovered their seats. It's a great way to freshen them up.
Knowing that the shuttlecraft can take on a bit of water, check your bilge pump for proper operation. Then dump some bleach or heavy cleaner inside and go at it with a pressure washer. That will remove the mildew that will form inside the hull. Then the smell is gone. I will take bleach smell over mildew anyday!!
Enjoy it, it's a fun ride. I loved mine and miss the heck out of it. Our new SeaDoo fits our current needs a bit better though.
Good luck!