Point to point or rail pass?

Definitely point-to-point in Italy. If you are confident in your travel days and can commit to specific times, you can buy your high-speed rail (freccia) tickets in advance for significant savings. See Trenitalia for tickets, schedules and prices.

12 days is not a lot of time for four major stops. Perhaps you can do Pompeii as a daytrip from Rome if that is your only objective south of Rome.

Count nights on the ground, your last day will probably be taken up by morning departure for travel back to your home.

Throwing a shoulder behind Laurel and Zoe: point-to-point is definitely your best option. I'll also agree that 4 locations is a bit much for 12 days considering that day 12 is probably your departure day?

Consider that you lose 1/2 day or more every time you change locations so doing so eats up more valuable sightseeing time than you might think. Pompei is a long day-trip from Rome but it's possible, or you might think about doing Ostia Antica instead? That one is much closer to Rome, can be done on inexpensive public transit tickets (or a 1-day transit pass), and many tourists have enjoyed it just as much.

How long to stay in each city depends on your interests: they're not same-same. Rome, for instance, is heavy on Roman ruins where Florence is a goldmine of Renaissance art. You DO need to buy advance tickets/reservations at the most-visited sites if you want to avoid long ticket lines once you arrive. Maybe you've done that already but as you mention that you haven't determined your length of stays, it doesn't sound as if you have?

What's a good website for purchasing tickets to major attractions in Italy, i.e. Coliseum? We are flying standby so everything we are doing is last minute bookings

As to websites, there are several you may need.

Coop Culture sells tickets to many monuments such as the Colosseo, but be aware there is still a long line to get through security to enter the Colosseo. If you book a tour you get in faster.

Walks of Italy is an excellent company both for touring the ancient area (Colosseo, etc) and for the Vatican (try their Pristine Sistine tour).

You can reserve the Galleria Borghese here.

Rick Steves' Italy guide has all kinds of info including websites and phone numbers for making reservations.

A few other ticket resources:

Accademia (Florence):

http://www.b-ticket.com/b-ticket/uffizi/info_venue_accademia.aspx

Vatican Museums:

http://mv.vatican.va/3_EN/pages/MV_Home.html

The Vatican Museums and Colosseum have the longest ticket lines in Rome so are the two you should pre-purchase for. Borghese pre-reservations are mandatory. In Florence, the two longest lines are at the Uffizi and Accademia; you shouldn't need to pre-purchase tickets anywhere else.

You will have to choose a specific day and time slot for the Vatican Museums, Uffizi, Accademia and Borghese. Tickets to the Colosseum (which also include the Forum and Palatine hill) can be used on your day of choice. They're also good for two consecutive days so you may visit the Colosseum on one day and the Forum/Palatine on the next day, if desired. You just can't split visits to the Forum/Palatine. It makes sense to do all of them on the same day, though, as they're in the same area.

If you can't plan too far ahead for tickets, there are brokers who usually have last-minute tickets.

The specific train routes of your plan make a difference if you're comparing ticket prices. If it is Rome-Naples-Venice-Florence-Rome, then you only need 4 travel days. Currently, you can get an Italy pass for 4 travel days for $159 per person in 2nd class, plus $48 per person for seat reservations booked sometime before boarding the train. Travel days can be spread over a window up to one month long; no need to use the days consecutively. FYI, only first-class passes work on the FCO airport train.

You're probably not going to lock in advance-discount tickets from home, since you're flying standby, but you may get lesser discounts by booking tickets a few days ahead, particularly for the longest leg. For instance, for travel this Thursday (in three days), the direct trains from Naples to Venice still have some seats at €69-89 per person.

The ideal would have been an open jaw tickets landing in Venice and returning from Rome, but I suppose you already have your air tickets.

If you already have air tickets in and out of Rome, go to the farthest point first (Venice) and work your way down south.
Day 1 depart from home
Day 2 arrive Rome. Immediately take train to Venice (3h45min journey)
Venice - 3 nights
(Train Venice-Florence: 2 hrs)
Florence - 4 nights with day trip(s) to Tuscan hill town(s) (maybe Siena?)
(Train Florence-Rome: 1.5 hrs)
Rome - 4 or 5 nights with day trip to Pompeii (about 2hrs journey each way)

It's 11 or 12 nights in total.

You are not staying long enough to cover more than a day trip to Pompeii.