... other than typical sensitivity. A week after having it in, I got a bad viral infection in my throat and sores on my tongue, and typical flu like symptoms. Since then (8 weeks), I still have swollen glands on that side. I have gone through extensive blood tests and am working with Drs. But my question here is, can having a silver filling removed and a new crown put in somehow cause an infection in my mouth like this? I'm just looking at all angles, and remembered I had the crown put in the week prior. Thank you

The answer to your question is no, the removal of the existing amalgam filling and placing of the crown will not cause the kind of infection you have.
Now, that being said, if the instruments that were used or if the dentist and/or his assistant were not wearing clean(fresh) gloves there is always a chance of something being transferred to you during the procedure. You might want to ask for a tour of the office to learn about their sterilization procedures.
There is a lot of what you are experiencing (swollen glands, flu-like symptoms) going around where I live right now so it could also just be coincidence. Hope you feel better soon.