If you have 3 full days there you can do quite a lot Anj. I've checked the weather and it's looking quite nice although cold of a night. But that'll be good for walking and sightseeing during the day. The heat and the crowds are the worst things about Rome but at this time of year you should avoid both, especially midweek.
For a good Catholic girl like yourself you should give the Vatican a full day. Getting into the Basilica is easy and also free. But I've never been to the Sistine or the gardens because the queues have always been horrendous. Not sure what they'll be like around now but I believe you can save time by booking tickets on line before you go.
Would also strongly recommend a visit to Ancient Rome to see the Colosseum and the Roman Forum. Again it's best if you allocate a full day for this. Both are magical if you like your history but are deffo still worth a look see even if you don't. It's not really within walking distance of where you're staying. Never used the underground and I've heard mixed reports on it too. But you can get a taxi or I'd imagine one of the tour buses will take you there.
A walking tour can also take in most of the other top attractions. I'll warn you it's a good hike, but Cal and I managed it in a day and it was 90 degrees so I'm sure it's doable. Walking down the avenue away from St Peters (where you can get some great pics of the Basilica) you'll come to Castello de Angelo and then take the magnificent Ponte de Angelo across the Tiber. Follow on from there to Piazza Navona, Rome's nicest Piazza imo. If you're a fan of Dan Brown's Angels and Demons this is where he tried to drown the Cardinal in one of the fountains. This is where you'll find some of the best restaurants too, which aren't too expensive if you stick to the pasta. From there it's a short walk to the Pantheon which again is a must see. There's also a nice Piazza here with decent restaurants. It's about a half mile walk from here to the Trevi Fountain, and it's well signed. From there you can get to the Spanish Steps. We managed to get lost so I'm not sure exactly how far this is. We ended up at the top of the steps but that was by luck more than judgement. The street from the bottom of the steps is allegedly shopping heaven and houses most of the fine boutiques. Luckily Cal was so wiped out by this stage that all she wanted to do was have a beer and park her arse. This street takes you back to the river where you can find your way back to Ponte de Angelo taking in the fine architecture along the way.
Hope this helps Anj. Whatever you decide to do I'm sure you'll have a great time.
