Unclear on your intent. If you are proposing these as round-trips, all to be accomplished within 12 days, I'd just say no to this plan:
1) In 12 days, this is simply too much to cover. You are correct when you say you are a newbie to intra-SE asia travel.
2) LCC's are more prone to delays and cancellations than the mainline carriers. You simply don't want to stake your holiday plans on Air Asia, Tiger, etc schedules. Not with such a short trip and essentially no flexibility to recover from IRROPs
3) This round-tripping out of KUL is a ridiculous plan. You'll spend most of the trip inside that horrible terminal. Don't force your trip plans into Air Asia's scheduling. If one-way tickets on other, more expensive airlines, make sense to prevent all this backtracking, then do it.

Cut it down. Phuket/Krabi and Langkawi are redundant. October for this coast is iffy weather-wise. You could get partly sunny, partly overcast/light shower days, or considerable rain. If a sunny beach holiday is a critical priority for you, you will be gambling with these destinations.

Hanoi and this area of Vietnam is prone to rain in late October-early November, sometimes with serious flooding. This can disrupt land transport though air transport not usually affected unless things are dire. South Vietnam and the HCMC area not usually an issue this time of year.

Flights in/out of Siem Reap are always expensive. Alternative airport is Phnom Penh/PNH which also has more availability. I'm not a fan of flying domestically between PNH-REP but it is possible. Road transport is plentiful between the two locations and with two of you, I'd probably just spring the cash for a private car (4-ish hours, decent road, probably about $50 total) rather than fart around with public buses. There are direct luxury buses between Saigon and Siem Reap (leaving each point around 7 am) with stop in PP. Assume it will eat up all day when you figure in border crossing formalities if there's a queue, but the trip is cheap, about US $25. Lots and lots of budget travelers do this rather than pay 8-10x more for the flight. You will see some countryside on the way. If going Vietnam-Cambodia you can get a Cambo visa at the border; the other way around, you need to have your Viet visa in advance.

A) Best suggestion for you is to cut this trip down to Vietnam and Cambodia. If you need a beach, look into Mui Ne in Vietnam. Phu Quoc may be possible but check on weather, and it's a bit more work to get to. Hoi An also has decent beach area, weather variable. I do not recommend Sihanoukville for beach in Cambodia. Do you have access to KA metal? If so, having your inbound destination as PNH would be possible, do Cambodia, then on to Vietnam with return trip home either from SGN or HAN. This prevents visa issues--remember that if you exit Vietnam for Cambodia then re-enter, you will need a double-entry visa (or new visa). I believe if you are flying into SGN on an intl flight then flying out on another intl flight, there is provision to transit visa-less, but check this with another source. And you'd need to get your timing right to avoid spending long periods trapped in the SGN airport.

B) If you must put an Andaman beach in the mix, I'd probably make in Phuket/Krabi over Langkawi. Scratch Hanoi completely due to lack of time. HKG-SGN and HKT or BKK-YUL. You can fly SGN-REP (VN) and REP-BKK (PG) then BKK-HKT (PG, TG, FD) but it will be expensive. Between locations, to balance time and cost, I'd either:
(1) Fly SGN-REP and overland to BKK (7 hrs now on excellent road) then fly on from BKK-HKT. OR
(2) Overland Saigon-Siem Reap with overnight/partial day in PP, then fly PG to BKK and then onward to HKT.

C) If you have not previously spend time in Thailand besides BKK, then consider Phuket or Krabi, another part of Thailand, and Angkor. A Bangkok Airways Discovery pass might be worthwhile for the REP segments, inexpensive options are available for Thailand domestic. You'll have to do the math. I've looked into things like Asean Airpass in the past, but it never comes out financially worthwhile.

If you want to store luggage for 12 days, you'll rack up enough charges to be meaningful. Don't store luggage in a country where you might have visa issues to get landside...like Vietnam. I think with my suggested plans and not so much focus on fitting your life around LCC requirements, the need to store a bag will go away and you can take stuff with you. You could handle the oddball single flight on an LCC with just one hit of excess fees. You might consider taking the contents of a large bag weighing over 20 kg and splitting it up so each of you has a checked bag under 20 kg, plus a carry-on apiece. Or consider shipping excess stuff you don't need for 3 months back to Canada by sea mail.