I am a registered veterinary technician, and I can whole-heartedly assure you that this has absolutely nothing to do with her being spayed, especially considering these symptoms came up weeks after her surgery. Spaying/neutering your pets is one of the best things you can do for them to keep them healthy!!!!
We have seen patients before with tick bourne disease that the owners claimed to have never seen a tick on them, either. I'm not saying this is what is is, just stating it could be a possibility. In fact, we had one come in today non ambulatory. Sounds like your little girl can walk, it just seems painful.
Forgive me if I've overlooked where you've said this, but have you brought her back in for an appointment specifically for her achiness??
Also, as Karen stated above, corn, wheat, and soy are the top 3 food allergens (beef is also a big one). Switching to a lamb and rice formula may be helpful for allergies. But I encourage you to not ignore the paw licking as it can cause sores and skin infections between her toes! Since she is 2 years old (and especially since she's spayed now) I do also encourage you to switch her to an adult formula as puppy food is high in fat and can cause weight gain.
Keep us updated, and no matter what never think you're a bad pet parent for getting her spayed!!!!
EDIT: I forgot to add - saw you mentioned you keep flea and tick meds on her. Depending on what brand/type of prevention you're using, most topicals do require the tick to bite the host before the product kills the tick. Then they typically die and fall off.
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