Howdy EC and welcome to forum!!!! Take some time and look through the site as you will see many people who have done rebuilds on their Starcraft transoms.
http://forums.iboats.com/forum/owne...ft-rebuilds-and-restorations-they-re-all-here
As for your particular boat, I am actually working on a SS16 as well. Doing a complete gut and redo. I haven't gotten to the transom install yet (So take what I say with a grain of salt); however, from all the research and everything I have seen here on Iboats it is very straight forward. From the pictures you posted, you should defiantly redo the transom. I would also check your knee bracket as I found mine was damaged which also augmented the damage for me as well.
So here is what I would do/am doing
First inspect knee bracket to make sure it is sound
I would also check all of your rivets and see if you need to replace/re buck (If you can) them.
Make sure you floors are sound and check for any corrosion.
Pull out the splash well. It is held in by rivets and screws. So nothing serious
Any foam you find you should look at putting it back in or replacing it with pink/blue foam (Closed foam) you can find at the big box stores
You will need to remove your motor and store it. You can find plans for motor mounts that others have built here on iBoats
Carefully remove the aluminum trim on top of transom (you can't find any replacements readily). So take your time and be careful
Transom should be held in by 3 bolts on each side, 2 transom eyes, and 6 knee bracket bolts. (Plus the 30 odd screws that the splash well had screwed until they pulled out
Once you remove all that hardware and you have the splash well out you should be able to pull the transom out
You will probably find that you will need to remove your corner stern brackets and bend the aluminum up to get your transom out.
Also, you should find three pieces in there that make up your transom. Hopefully they aren't shot so you can use them as a template to make your knew transom. If not you can use cardboard and trim away until you get the size and shape you want to fit back in and use that as your guide.
Reinstall
So you will find that most of the guys here use 3/4 CDX (exterior grade plywood) and glue two sheets (Cut to size) together to get the 1 1/2 inches needed for the transom
Personally, I do a lot of wood working as a hobby, so I plan to build and glue my two pieces together larger then what I need. Then once dry cut them as one piece so I don't have to worry about one being slightly bigger and doing a lot of sanding. Guys have done it both ways, just have to figure out what is best for you
Some use epoxy with mat to glue the pieces together, others use Tightbond III and a lot of stainless steel screws (Personally I will be going Tightbond route as I have that available)
Then you dry fit mark your holes and drill them out (Not while you have it mounted). You will also find some of the guys have over drilled their holes and then filled with epoxy and then re drilled with the size they need so there will be no way for the water to get in
Once you are happy, you will need to waterproof is so that you won't have to do this again
A lot of guys you will find use epoxy, some you polyester resin with glass, others use marine varnish, and others use paint. It is up to you, but I will be glassing mine when I redo it.
Once you have completed your waterproofing, you reinstall and everything in reverse order and you should be good to go.
I have seen guys say they could get it done in a day. I don't know about that, but its up to you.
So from my limited experience/research that is how I would look at doing it. JMHO I am sure some of the other guys will chime in and correct anything that I misspoke about, but you get the general idea. It may seem overwhelming, but in the end isn't the hardest thing. Plus these guys on this forum are great and will defiantly offer any advice you need.
