Hi c4c!
This might not help you directly (sorry!) but may give an idea that could be adapted to your needs...
Our respective multifuel stoves are a little different, but mine stores in aluminum pots that nest to form a carry-case and hold the entire lot of my cooking gear, including Swiss Army Deluxe Tinker knife, MSR piezoelectric igniter, cleaning sponge/scouring pad, bottle of pump oil and two folding spoons. The stove has never leaked to date, so no danger of getting fuel on the pots, and when used as a case the pots protect the burner from damage and my bags from burner soot. If burning naphtha or unleaded petrol, the pots don't get sooted, but I carry the lot in a lightweight roll-top dry sack anyway to ensure my panniers stay clean and this comes in handy if I have to burn "dirty fuels" like kerosene/paraffin.
c4c, in looking at my setup, I wonder if you might be able to wrap the burner assembly and fuel hose in a zip-top plastic sack and then store it inside your pots? Another possibility -- though it would take the place of a water bottle -- would be to put it in a plastic lidded container and strap it to a Salsa Anything cage outside the bags. Depending on how much room is needed to contain the burner assembly and supply hose, it might pack into an empty Gatorade powdered mix can with screw-on lid; those are almost purpose-made to fit an Anything cage and would be very sturdy and weather proof as well, being made of polyethylene with a labyrinth-gasketed lid.
As for the fuel bottle itself, I realize if the lid contains a valve assembly it may not be secure (as you've found). Hmm. Perhaps it could be carried in a bottle cage secured with either a tether, mini-bungee or toe strap or in a BikeBuddy cage/mount (
http://bikebuddy.co.uk/ ). Topeak do make a couple of bottle cages with adjustable capacity and it might be possible to snug such a cage 'round the fuel bottle, adding security.
This next idea is Out There a ways, but a question: Would a Trangia or similar spirits/meths/alcohol stove fit your needs? The stoves can be fairly inexpensive (my Mini-Trangia kit was USD$10 on sale, complete with stand, pot, and frypan/lid). Fuel is widely available and lacks many of the problems associated with petrol-based fuels; it evaporates cleanly with no real odor if spilled. It doesn't have the energy density of naphtha and so is less economical for long trips away from resupply, but can still do a fine job if it is not going to be very cold and if you can carry enough fuel or can replenish it at intervals. A Trangia with, say, a Clickstand support/windshield should still work with your current pots and pans and these are available fairly inexpensively -- really inexpensively compared to higher-end iso-butane stoves and are an especially good bargain compared to most multifuel stoves. It can be made to simmer and will burn a considerable amount of time on each full fill and can cook rice and beans if those have been softened a bit first. I have a Mini-Trangia kit for use up to about three days and a Heineken beer can penny-stove for day rides and overnight (8-minute burns per fill), this last used with a small set of nesting alu bowls to boil water for tea and to cook my preassembled freezer-bag meals that are then steeped in a homemade Reflectix cozy.
Just some general thoughts on stove/fuel packing/placement, hoping something among them might prove helpful to you.
Best,
Dan.
