For the work out program do I need all the required items in order to do/start the full complete program?
You can do the program with less gear and sub in other stuff for sure, that won't be a problem, an additional option would be to start the program and do what you can do the first time and then you can restart the program as many times as you would like for a year from your purchase date.
GARMIN or Apple Watch?
I personally have a Garmin 735 xt, but I have heard good stuff about the apple watch. Never tried it though so I can't give an opinion about it.
Does the “2mm” or “5mm” nylon dive boot size matter? Or is it just preference?
Whichever you can get that is cheaper will work, it's just there as a sock for your fin to prevent blisters.
Are the boots you have listed on your website under equipment tall enough? The Lowa Men’s Zephyr GTX Mid TF hiking boots or are the “mid” too low?
Depends on what you like. I have worn those in uniform for a long time. Also, just remember most people have field boots and garrison boots. When you are in the field, you unblouse your boots.
I was wondering what physical benchmarks I should be at before starting training, as well as what gear I should be buying?
In order to start the past program there are not specific benchmarks but I usually tell people as long as they can pass the AF PT test then they will be just fine. Also, you can repeat the workout as many times as you want for up to a year from your purchase date. Equipment recommendations can be found on my website here or on my amazon page here.