First off, congratulazioni on your upcoming wedding! (OT but I always find it fascinating to witness Italian newlyweds in Rome. I've seen them, still dressed in there gown and tux, posing all over the city on their special day. Charming!).

I've inserted numbers in your posts to make it easier for me to attempt to help - here is the information that I'm aware of, along with my completely subjective, singular opinions:

(1) If you intend to visit the Borghese Gallery you will need to prebook. (In general, I don't like pre-booking and I hate pre-paying so I avoid this whenever possible).

(2) Yes, you can skip the line at the Vatican Museum by pre-booking. What I did was prebook the tour (I originally was tipped off to this by some Roman acquaintances who would book the tour in order to bypass the long lines and then would just ditch the tour once inside). However, I see on their website now that by just making an entrance booking that you also bypass the lines. (And I have full confidence that the Vatican machine would be honest - with their claims of avoiding lines that is )

Regarding the lines at the Coloseum, you can avoid it by buying the ticket at the Palatine, buying the RomaPass, or buying the Archeological card.

(3) The Roma Pass is a savings for some people, those that pack in alot of siteseeing in a short amount of time for example. It does not save me anything, rather, it would be more costly than my other choices. You sound like you have a clear idea of what you'd like to see and how you'd like to pace yourselves, so you just need to add everything up and see which costs less. I assume you are already referring to these sites for prices, opening times, etc:
http://en.turismoroma.it/
http://www.060608.it/en

I find the Archeological Card to be the best option for me.

The 3-day unlimited transportation feature of the Roma Pass can also be quantified helpful or not. Your location is ideal, and if I were staying there I wouldn't be using the metro or buses except for when I went to the Appian Way or further. I might grab the metro here or there if I wanted to get from the Vatican to the Palatine for example, but that's a cost of €1. If you're the sort that doesn't like to walk you may want to consider the 7 day "CIS" ticket which gives you unlimited metro and bus rides for €16: http://www.atac.roma.it/index.asp?p=19&i=14. But the magic of Rome is found by walking through its streets, not by sitting on its crowded buses and taking its limited metro which will have you doing the Termini shuffle gauntlet to change from its Line A to Line B... I avoid it as much as possible and your location IS really ideal for you to avoid it as well (except, as mentioned, for your outings outside the city center).

(4) What guided tours are you referring to? This is a very general question. Some are worth it, some are not. It's dependent on the quality of the tour but also, it depends on what your interests are. Some people seem quite content to just gaze at sites and walk past them. Some people enjoy learning about what they are looking at. My interests are the history of Ancient Rome, its architecture and art. Therefore it was worth it to me to have several Context Rome tours (and I am budget minded too). Based on the sites you are interested in you may also be interested in booking one of CR's tours. As mentioned, the groups are small, 6 ppl, so one afternoon spent doing this may be a worthwhile splurge and a nice option for you two.

Conversely, my interests in the Vatican Museum were completely addressed by the tour offered by the Vatican itself and I appreciated the economical price which included admission as well. I found this museum to be way too crowded and overwhelming and so was very happy to be led around and navigated through the mass of humanity. And I found the Vatican guide to be well informed, enthusiastic and very able - and I had much more confidence in the quality of the information that I was receiving from her, as opposed to if I had picked some guide hustling outside the museum walls. Lastly, I see now that they also offer a tour of the museum combined with a tour of the basilica for just €5 more - for me this would be very interesting and I find it relatively economical as well: Vatican website Ticket Office

My favorite museum is the Capitoline, and there I'd hate to be led around on someone else's timetable. I posted recently on a ST thread comparing the Borghese to the Capitoline (my ST user name is Jady): Borghese or Capitoline

I would think a good option for you two at many of the sites would be to rent one audio guide. It's like a cordless phone (no headset) so you could share it between you and get the cursory info and remain in your own newlywed world, so to speak.

And a general suggestion - on your first day when you are still jet lagged you could take the 110 Open-Top Tourist Bus. The idea is to take the ride the full route, without getting off, so you could get your bearings in the city and you'd see all the sites (and the traffic!) and could just sit there and be groggy while enjoying the excitement that you are there! Married and in Rome!! Here are the links:
http://en.turismoroma.it/benvenuti_a...citta#110_open
http://www.trambusopen.com/en/110open.cfm

I'll continue this post later.....