So I had some tomatoes that were in containers and they start to wilt, didn't think to much of it, but then they never recovered. After pulling them tosay, I noticed a couple bore holes in the stem. Who's the culprit?

Your pests are one of the young growth stages (instars) of the scentless plant bug, Niesthrea louisianica, also commonly referred to as seed bugs because they prefer to feed on the seeds of mallows, including Rose of Sharon and Hardy hibiscus plants. They are generally harmless since mallows produce gazillions of seeds each year and no one tends to want 1,000 new volunteer seedlings each Spring. Also, these bugs are great at controlling the related invasive weed, velvetleaf, as studies show the scentless plant bugs will eat/destroy over 95% the the seeds produced by velvetleaf. If you don't want them on your plants, a simple insecticidal soap spray ought to take care of them.

I just had japanese beetles eating my basil

A lot of different species of beetles (these are ALL scarab beetles here) are called June bugs and what is called a "June bug" is mostly based on where you are. The metallic green ones like you posted are the June bugs of southern California. I love those things, no matter what they're eating. Move east and June bugs look like the little guy posted above. And they are much more common.