Oh man, I'm sorry to hear that! Some cats are much more sensitive to any type of "handling" than are others, even if there is no pain involved at all. Thank goodness my diabetic cat is the easy-to-handle one, because my other cat is NOT!
Sometimes it can help to focus on what it feels like to you when the needle goes through the skin. Generally you'd feel a tiny bit of split-second resistance and then the needle slips under. You have to stop forward progress immediately at that point because if you push the needle beyond that, you could hit underlying muscle tissue. This is more likely to happen on the cat's back or hip or side than on the scruff, because in most cats, the scruff has lots more loose skin. (It's also often tougher to pierce the skin in the scruff than other spots, so you might be pushing the needle through with more force than necessary now that you are shooting elsewhere.)
Also, I know the official recommendation is to pull back on the syringe to check for blood, but I NEVER do that. I was a tech for many years and didn't do it at work either (nor did anyone else). The odds of hitting a vein while doing a SC injection on a cat are miniscule as long as the skin is being pulled up a bit. In your case, it's probably really complicating your injection process because it adds more handling time and annoyance for the cat.
My cat doesn't mind the shots at all, but he doesn't particularly like the blood draws. His reaction is just to fidget or pull his ear away, but of course that makes getting test strip to blood drop harder! So what I do is take a small bit of smelly fishy food, like maybe just 1/2-1 tsp, put it in a saucer, add water and stir it up to make a fishy broth. Then he stays busy lapping that up while I do my test. (Lots of people like to just use a treat afterwards, and that's great for rewarding a cat after the behavior of remaining still, but it doesn't really help with a cat that is having difficulty during the procedure. Also, giving treats tend to make my cat jerk around looking for the next one.)
I'd recommend that you try doing some conditioning/desensitization work with him outside of testing/shot time. Multiple times per day, set up your towel on the counter (or whatever you are doing for your testing/shot spot), call him up there and give him a few minutes of fishy broth time (or whatever he loves) with no other handling at all. Then after a day of multiple sessions like this, start doing gentle petting while providing the broth. Work up to petting more firmly, and then start tenting his skin. The more often you can condition him to the idea that the testing spot is a good place, the more he will become conditioned to feeling neutral or positive about being there, and accepting of your handling.
I give my cat his shots while he is eating in his regular food spot because it's easy for me and he doesn't mind, and you may find that yours doesn't notice getting a shot while his head is in the bowl. I'd try it once or twice to assess. If he seems to be reasonably okay with that, it might be a good plan moving forward.
If he is not okay with it, I would do a whole lot of CC/DS sessions there before trying again. You don't want him to associate your approach with getting a shot that he doesn't like while eating, because we always want our cats to feel calm and safe at mealtimes.
Normally when doing counterconditioning and desensitization (CC/DS), the owner would avoid doing any handling that stresses the cat throughout the entire process, so that all experiences can lead to the kitty pairing good things with the given situation. In your case, I realize that you will still have to do your regular injections and testing so you won't be able to follow an ideal CC/DS plan. So the best you can do it to overpower the actual stressful times in his mind with way more non-stressful CC/DS sessions.
