You will need to build such shipping crate, 1/2" plywood is usually the standard material, wood stud frame 2"x2" studs sould be good. You want to build the crate very sturdy but also you dont want to make it to heavy if its not needed, also not to small but not to large.
Design the crate so the the plywood lid can be taken on and off, you will want he lid to be held closed with wood screws that can be easily removed with a screw driver.
Use wood studs on the bottom so that the crate can be picked up by the hilo at the airport, also so that you will have a place to grab and carry the crate by hand.
As far as the crate's size, well if you are shipping a 36" crocodilian then I would suggest that the crate's length be 37"-38" but even a crate's lenght is "slightly" shorter or "slightly" longer than the crocodilian it should be fine. In regards to the crate's width you dont want to have to squeeze the crocodilian into the crate but you also dont want to make the crate to wide as it will allow the croc to move about the crate to easily (turn around, etc.) for example if the croc is say 6" wide at its fattest point then I would make the crate maybe 2" wider so about 8" or so wide (making only minimal movement possible).
About padding, its not required by IATA regulations, but it IS surely a good idea to do so as the croc will almost certainly thrash its head about durring shipping causing nice little cuts and scrapes to its nose if you dont use padding. You can use those pink insalation sheets as they will provide the needed padding, they are fairly low cost and easy to work with, you can cut the sheets to fit with a utility knife then screw the insalation into the frame or just staple to the plywood, the padding is really only needed in the end were the crocodilians head will be (top, bottom & both sides) but I usually just do the whole inside of the crate just to be on the safe side.
As far as ventilation goes, I believe IATA only requires air holes on 2 sides, but USFWS has told me that they prefer and think its best for the animal for many airholes to be placed on all 4 sides as well as the lid, make the air holes about the size of a pencil or slightly larger.
You will also want to write (with perm marker or paint) "live reptile" & "no harsh temps" on the outside of the crate make it visible, all 4 sides and top is probably best, also it may be a good idea to put both the sender & receivers name & number on the crate in case of any problems.
Wow, that was long, IATA pics would have been easier, anyway I hope that helps.