Well, at the risk of getting trampled in the stampede, & hoping you haven't given up, I'll put in my 2 cents: My experience with patching anything that involves rotten or rotting wood is that it's throwing good 'money' (time, energy, materials) after bad. I wish you, & your parents, the best.

Just a few quick ideas. The area looks somewhat shaded to grow the cuc, tom and peppers. They need full sun most of the day for best production. Lettuce, and other leafy vegetables, should work in the area however. Adding a layer of single poly over the area in winter will not help much with temperatures. A poly cover in spring and fall may give some additional growing time, but probably not in the winter. The inside/outside temps. will be the same only a few hours after sunset. Adding any kind of animal netting around your garden area will be a benefit. However, Ground squirrels will just dig under it, and tree squirrels ( you did not mention which one you have problems with) can just go over the fence, unless you also have a fence cover over the top. ( I have both problems....)

I'm fairly new to this forum altho have gardened in various ways for many years but your post brings some questions to mind. I'm curious about the size of your "garden" - will that be large enough for the plants you are planning? I find that quite a small garden and would probably use those 2'x10's and make 3 raised beds which are not so tall. Unless your base is pure bedrock you won't need more than 8" of good soil for most plants. If you loosen the base with a fork it will improve over time. Of course there may be another reason you want to elevate the garden to make it easier to work but you really don't need IMO to have 28" of good soil. If you have any reasonable soil you could fill the tall bed with greens and browns mixed with soil and top it with 8"-10" of good soil, whatever is available. Any worms in the soil will have a feast. If you start a compost bin ASAP you will have some good stuff to topdress your garden in a few months. I've rarely come across bagged soils that are all that good at a low price, and I think it might be a pretty expensive way to garden if you buy that much at high prices. Better to buy some organic fertilizers to supplement until you can get that compost done.

I thought of using cedar, but when I priced it, it was way too expensive and didn't make sense to do it. And I'm sorry to say, but if you're trying to grow as much food as you can, two 4x4 beds are not very much and I think that is a lot of money for two small beds. I have one long bed 12" high, 11ft long and 4ft wide. I have four beds 12" high, 4ft x 4ft. I made them with Pine because I had some already and didn't have to buy much more. It's actually been about 8 years since we built them and they are ready to be replaced now. Now I want to double the square footage that I can grow in. So I want to build… Two beds 12" high, 16ft long, 4ft wide Six beds 12" high, 6ft long, 4ft wide That doubles my growing space. I don't feel I need deeper beds, because vegetables are annuals and I've read somewhere recently that they don't really need 18" deep beds. 12" is just right for me and I don't mind bending and kneeling. So less wood. I priced what cedar I could find and it was going to cost me over $600. to build those beds. I called 12 lumber yards and only two had cedar and they weren't the dimensions I wanted either. Finally, one lumber yard, said he was steering people to use Eastern Hemlock rough sawn, which is very inexpensive. It is more rot resistant than Pine but less than Cedar. Estimates were 5yrs for Pine, 8-10 years for Hemlock, and 15yrs for Cedar. I priced the Hemlock and it was going to cost me $198. to build the same beds. So, if I built the hemlock and had to replace them in 10 years for another $200. It would still be $200. less than building the cedar beds, and would last me 5yrs longer.