If you feel like the vaccine may be contraindicated by your history of lyme disease, definitely check with a doctor first. We are definitely not familiar with lyme disease here as a general group. If it is just people on the internet saying to stay away from the preservatives and such, getting that special one you mentioned is a good compromise. But anyone who is extra susceptible to respiratory illness can suffer terrible complications from the flu, so you just have to weigh the risk vs benefit as you have to do in most medical decisions.
The laboratory standards changing is something I have heard of. This year there was a lot of controversy with certain insurers looking at patients who were on IVIG treatment and therefore had normal IgG levels, telling them "hey you are normal now so we aren't paying for IVIG anymore you need to be reassessed after a 6 month break" and totally screwing up people's lives. I suspect that has something to do with all of that and more standards being put into place to try and protect against that.
I saw my Lyme doctor and he said the flu shot is ok so long as I am not sick in the sense of having fever or overt symptoms. I still have to find an immunologist in my area. This recent bout of upper respiratory infection really knocked me down hard so I cannot afford to get the flu, I could lose my job if I keep calling in sick.
What surprises me is that all of us with celiac and perhaps other autoimmune issues should be checked up front for these deficiencies. I have gone all my life not knowing I had celiac until my 40's. Then found out I had Lyme for who knows how long.
I say all of this because I hope others are reading/following this thread because I have a feeling many can relate to being sickly all their lives and not understanding why, then finding out you have celiac and thinking "ah ok, well this explains alot," only to keep getting sick and not feeling better after going strictly gluten-free. THen you start peeling back the layers and there is Lyme, immune deficiencies, detox'ing problems etc etc.