All the neurochemists on the forum should be answering any minute now....
My experience has been that we tend to use anything that feels good in the moment addcitively. I don't think you're harming your recovery in the short term by drinking coffee and smoking camels, but later on down the line it's stuff to look at.
In Narcotics Anonymous we lump all drugs together and count clean time if we're abstinent from all of them (including alcohol). Caffeine and Nicotine get a free pass, and so do medications that aren't controlled as long as we're not abusing them.
My own personal experience is that I quit using alcohol and other drugs. Then with about 8 months clean I quit smoking. I tried energy drinks for a hot minute around that time and found that they felt too much like using (to me), so I won't drink them. A little after two years clean I changed my approach to romantic relationships as that was making my life unmanageable, causing harm, and definitely fell into the category of "using". Caffeine hasn't made my life unmanageable, but over-eating has, so I'm addressing that one now.
My sponsor told me a long time ago that we address our addictions in the order that they are killing us. In terms of counting clean/sober time, I don't have to start at day one again as long as I abstain from alcohol and other drugs that would get me loaded. However, I don't want to cause any more damage to myself or others, so it's important for me to not smoke and maintain integrity in my relationships.
Not saying that one can't go for broke and quit smoking and drinking coffee while getting clean and sober, but for a lot of people it is tough enough to quit getting loaded, and that's what's killing them the quickest.