After reading this thread, I remain convinced that boiling is the best overall means of sanitizing water. Using my Pocket Rocket canister stove, I can boil two cups of water in four minutes, taking care of everything except some chemical impurities. A side benefit is that it is very easy to produce that essential nice cup of tea.

You want to get water into your bottle without contaminating the threads. How about a funnel?
Gas stations usually have paper funnels available if you need to put oil in the car. Check your local quicke mart and see if you can get a couple. Look where they have the section of overpriced motor oil.

Is there any of the individually packaged hand wipes that have chlorine in them? As that would at least help to wipe the threads. I have Benzalkonium Chloride wipes in my FAK's, would they do anything to sanitize threads of the bottle? If so you can buy additional wipes at any medical supply store and I think REI also has them.

As others have said, treat the water by simply sloshing water on the water bottle and lid threads. Works for me and untold numbers of hikers and outdoors people around the world...

I use the brand of Aquatabs purification tablets. These only need ~1/2 hour to treat the water. In Canada, the tablets can be found at MEC where they cost $8.75 for a pack of 50 (expiry date 2014) and each tablet will treat a liter of water.

A filter is quicker and easier and doesn't use valuable fuel. Some smaller filter can be up and pumping in the time it takes you to pull them out of your pack. But, that out there as context, boiling has a lot going for it if managed well.

Instead of using a liquid, or gas, fueled stove you could use a solid-fuel stove like a Sierra Stove. Surrounded by softwood forests that have seemingly endless supplies of dead-fall, and wood frame houses that can be expected to be leaving a lot of nice woods lying around for anyone to collect, fuel is not likely to be an issue. After your first use you have a small supply of charcoal that makes getting the unit burning hot very fast. Speed and fuel don't seem to be issues.

Also, once you have boiling water disinfecting canteens and equipment is simple and making tea or coffee, always helpful in any crisis, easy. The small fire is warming, can be used to dry damp socks and the small amount of smoke helps keep mosquitoes and gnats away. With nearly unlimited fuel around the only limit is batteries. The small fan runs a long time on a single battery. In comparison with fuel weight and bulk are much more manageable. Use rechargeable batteries and a solar charger to keep them charged and stove use would be close to unlimited.

A wood burning stove and a backup of a small filter, like the filter straw, and a short supply of iodine might be well adapted to some situation.

If you are going to be on the move through an area that prohibits open flame, then clean water discipline can take some thought. If in this situation, I try to carry a lot of good water from the outset and avoid having to treat if I can. If this is impractical, then you have to accept that your raw water gathering gear is going to be contaminated and must be kept separate from the water you clean.

Starting with a clean filter set, I carefully remove the cap on the output spout and hook up the output tube keeping it from touching anything but a very large clean water container or two. Then I put on latex gloves to set up the intake for the filter pump and begin pumping; I assume touching anything while gloved contaminates it.

When the clean water container is full I carefully remove the gloves to avoid contaminating one bare hand, and with that bare hand remove the output tube and replace the output tube cover. I place hopefully still clean the output tube in its own plastic, water-tight bag. Everything else goes into another waster-tight bag which I assume is now contaminated throughout, along with my hands.

I use alcohol based wipes to clean my hands and hope I only have to process water once this way before getting to an area that allows open flame so boiling water can clean the gear and me.

Edit: extended exposure to the UV in sunlight is supposed to do a decent job of decontaminating see-through components and outside surfaces of your filter set up.

Remember with cups, pots, pans etc that the sun will kill all bad guys with UV light in a very short period of time. So even if you wash your pot in 'contaminated water', setting it in the sun will kill everything.