12:08 p.m. on March 24, 2011 (EDT)
No simple answer, since the airlines seem to be changing their policies daily. My first question is TWO weeks for Denali??? I guess this means a backpacking trip rather than a climb, since most people allow at least 3 preferably 4 weeks for the routes from the south and 6 weeks or more if they are doing the route from the north (crossing all the rivers) or a traverse.
But to your questions -
TSA changed the rules on stoves last summer. You may take your stove and fuel bottle in your checked luggage if they pass the "sniff test". Even on Alaska Airlines! (Alaska used to forbid and actually confiscate stoves and fuel bottles, even brand new in the original shrink wrap). Look on the TSA website and print out the page. You may not bring fuel, obviously. This means you cannot take butane canisters, of course, but you can buy these in Anchorage at Alaska Mountaineering (on Spenard, just north of Northern Lights Blvd - ask for the Ice Dawg for great personalized service, he used to be a regular on the old rec.climbing.useful). REI is in the big shopping center at the SW corner of Spenard and Northern Lights.
You will probably need to spend a day or two in Anchorage before heading north. I used to suggest Earth B&B when Margriet owned it. She extracted a promise from the folks to whom she sold it that they would continue catering to hikers and climbers, but I haven't been there in a few years, so don't know the current situation. Their website still says "climbers". The alternative is Alaska B&B, which is more of a backpacker's B&B and a bit funky, even for climbers.
When Barb and I went up in 2004, we sent the tent, stove, and some other heavy stuff by UPS ground a week ahead of time to Earth B&B, then sent it back at the end of the trip by FedEx ground (turned out to be cheaper than UPS, plus the FedEx terminal is right on the airport). This was partly because it was while Alaska Airlines was still confiscating stoves, but also because of the weight issue. Best bet for shipping is contact the B&B you reserve at for the first night or two and make arrangements to ship to them and hold it for you. On return, take it to a main office of UPS or FedEx. Use TSA locks on the duffel, or better yet, get a fairly sturdy box to put the stuff in and have the B&B store it for you while you are on the hill.
One of the changes by the airlines is the luggage charges. The size and weight limits, plus potentially charging for the first bag, and maybe a limit on economy passengers getting only one checked bag, make carrying your gear potentially pretty expensive. Last night, one of our local TV stations had a bit on the baggage charges. The size limit is now smaller than a few years ago for both checked and carryon bags. The measurement includes wheels and handles if they protrude - potentially a killer. Exceeding the size and the weight each count, so you could potentially pay a double penalty - if I had been over on my Antarctic trip on both, I could have paid an extra $90 x 2 for each of my 2 checked bags (luckily, I was within the limit on both). I suggest getting one of the small hanging scales that you can stick in your bag to check the weight on return before getting to the airport. Certainly check your airline for their current limits and charges and carefully weigh and measure the bags.
Based on many years and many flights, I strongly suggest getting sturdy duffels to put your packs in - some people have no problems with the conveyor belts and baggage gorillas, but some people on almost every flight I have been on have had torn waist belts, shoulder belts, or other straps. I also use a roll-around bag (Eagle Creek brand) for use in the airports. The B&B in Anchorage will probably let you store the duffels while you are on the hill.
Be sure you use TSA locks. I prefer the ones with the indicator to see if the bag has been opened. YES! to your question of "does TSA open the bag?" They seem to like bags with climbing gear (ice ax, crampons, snowshoes, and even hiking poles). They will leave a note with an address if you want to make a claim (good luck on that!). I have had them open the top pocket on the pack and lose stuff out of it (luckily I found the items in the bottom of the duffel - another reason for using an outer duffel for your pack).
Getting to Denali - best bet is to take Alaska Railroad. Since I think you are likely to be going backpacking in the northern part of the park, you take the train to the town of Mt. McKinley National Park. From there, you take the park bus to your assigned sector (you get this from the NPS either before you go - best plan, or walk to the NPS building from the train station - there are campsites near the office). You can't drive to Wonder Lake, so a rental car is just an extra unneeded expense. Besides the train is a really fun way to go, with chances to see lots of wildlife from the train. And it is cheaper than a rental car.