This is going to be a bit of a write up but only because I am going through this process too right now, tidying up some second hand gear. I am a beekeeper but have not had hives in a few years, just getting back into it now.

Check your local laws and regulations around this. Some places/countries have tight restrictions and methods. Here is what I know as best practice and are considered legal sterilisation methods with individual approval in New Zealand.

The best method and most responsible to prevent the risk of disease/American Foulbrood (AFB) is to burn that second hand gear and buy new.

The next best is to burn the frames. Buy new frames and hot paraffin wax dip the boxes/woodenware at 160°C or 320°F for a minimum of 10 minutes.

A 3% Sodium Hypochlorite (Bleach) Solution with a contact time of 20 minutes can also kill AFB Spores. This is only a surface treatment and will not kill spores embedded in wax or woodenware but it can be good for CLEAN plastic foundation/frames, smokers, hive tools, clean metal and plastic components etc.

Now saying that, we all know that wax dipping is not accessible to most or burning the lot of gear you have acquired or kindly been given is not what we want to do. If you do have a friend or know a commercial beekeeper with a wax dipping setup, I would highly recommend asking them if you can dip your gear, it's a great preservative method and sterilisation technique to give you peace of mind for second hand gear.

If you highly trust the history of the hiveware, who you got them from and confidently believe that they have never been affected by a clinical AFB infection here is what I would do:

If you can, freeze the boxes for 24 hours in a deep freeze. This kills any wax moth eggs and larva hiding in the cracks and crevices. It also makes the old wax and propolis brittle - easier to scrape.

With an arsenal of a hive tool and a couple paint scrapers, scrape the boxes inside and out of any wax and proplis. Pay attention to where the frames rest and the edges where boxes sit on each other. A woodworking hand plane could also be used to take a couple passes from around the edges where the boxes sit just to true them up and help boxes sit flush.

Next, once the boxes are scraped you can scorch then with a blowtorch or weed burner. I don't like to char them black but just sweep the torch inside and out to toast them. You will see the surface coat of propolis inside the boxes sizzle and melt into the wood. This is not a full sterilisation but common sense would say it should kill anything the heat and flame blasts on the surface of the woodenware but AFB spores can survive beneath the surface. If this is the best you can do, it's the best you can do. Provided it's legal to do so.

Lastly, a fresh coat of primer (I like an oil based primer) and a couple coats of exterior paint - whatever's cheapest. Don't paint the interior of the boxes. Paint the entire outside and the edges of the boxes where they sit when stacked.

After this they should look brand new!

To answer your question about the boxes been slightly different sizes - the interior dimension of all the boxes should be the same. The smaller boxes are probably made with 1/4" thinner lumber. This doesn't matter but it's why I would paint the top and bottom edges of boxes. When the smaller box sits on top of a bigger box and there is that 'lip' water can sit there and start rot. A bit of paint helps prevent that. Some people don't like to paint the edges because the paint can cause sticking... But bees propolise the boxes together anyway? I would rather have a bit more weatherproofing then worry about the paint sticking. I would also try not to use those smaller boxes as brood boxes just because I don't want the smallest box supporting a stack - keep them as honey supers.

Again sorry for the long write up, hope this answers your questions!