How much can I realistically expect to pay for a complete bike without the latest, greatest, components?
How you define that statement as it relates to the components will really be your driver you can add a lot or a little beyond the frame prices. You have established a internal sense that the Silvio style bike will meet your riding desires and you are coming from an S2 Carbon experience. So you cost drivers will be Wheels; Brifters, Tires, Derailleurs, Safety gear, Cabling. Each item you lower the grade on will have a different impact on the result. With Wheels being the speed; and drive train being about "the clunk" in your ride.
A key item to realize is that a tricked out Silvio is going to be able to run with a Trek Project One bike and hold it's own; and it isn't going to cost you $13k, but it also isn't going to cost you $3k. So it's going to be 1 tier up from the S2's low end configuration and about the same as a decked out S2.
You can get a full bike built to spec from a number of sources including: ViteBikes, RoseCity, SpinzCycle the later two have a presence here; and I'm sure there are others; all three can ship you a complete bike and you would only have to dial in the boom. The Bent community is also pretty cool; if you can find someone local the might help you do a build.
There are not a lot of Silvios that come up used; but in the last 4 months there have been 4 by my count; 3 for ergo reasons didn't work out; and 1 person that went back to DF riding. Each one took about a week to sell; so there's time get in on the game; They hold their price well so you won't save a ton on used and you don't get to pick the components. Someone one is always upgrading, The Vendetta is looking awful tempting to me, so I'm sure there will be more used ones if you are patient.
If you want to do you own build; it's actually not that hard; and I did a complete documentation on the project including costs and a spreadsheet to let you substitute your own parts. It's over at BROL http://www.bentrideronline.com/messageboard/showthread.php?t=104477 you have to sign up to view the pictures inline on the web; but it's free. My wife built her's using my guide. She did the frame and components all on her own and she'd never adjusted a derailleur in her life... the key was we did it in the winter and took our sweet time. Mounting tires on the rims was the only thing I had to do for her.
So you have options; but you should be able to settle in on a solid config for $4k-$6k project complete. So that's the answer to your primary question. You simply won't get under $4k with the new frame price and have something you'll want to ride when compared to your S2. (This assumes you use name brand components, I'm excluding no name clone parts as that's a personal risk tolerance decision).
Lastly you said you have a shoulder injury, you might be very well served getting a Quest 20 or 26; and trying out the platform before taking the Silvio plunge; the June sale is a great deal; the bike is complete. If you ride it; adapt and love it; then you have alot of options. If it's not compatible with your shoulder (other have had issues) you have avoided a disappointing detour. I have a bad shoulder and neck and I do fine, results vary. In either case you'll have an easy time selling it and upgrading or bailing. Quests rarely come up for sale and they vanish fast.... Or you do like we did; we have Quest's for utility riding and Silvio's for running long and sprinting. The Silvio is only getting better and better with each iteration so no harm in waiting.
For the record the guy around the corner from my house commutes on a Rans Rocket; he's 6'5" never saw a Quest before; we squeezed him on the Quest 20" and he was riding around the parking lot in 10 minutes. So it seems the Rocket to Quest is an easy transition.
That's my $1.05 on the question; estimate value to you will vary :) Oh and welcome to the bent side of life.