Hi Dennis
I have a long history of trying to get a good cup of coffee. Thought I'd share a few of my commonly used techniques.
I buy organic but I always rely on a quick but very energetic wash under running cold water with the beans in a sieve. I grind them in a table top grinder and keep them in it but you could have a go with a mortar and pestle. I have one made from stone with loads of fossil shrimps in it!
I avoid anything that is dried/powdered as I have problems with the sulphite preservatives used for dried food. If you can't find a wholesaler/marketer who will sell you beans from a sack try opening the packet with scissors without disturbing the seals. If anything has got onto the beans from the packaging it should wash off again. I use the glass steel filter coffee pot but I don't think they use latex when boiling water is concerned. With tea I put leaves and water in the mug and then microwave it for three minutes. You could test your system on different foods to see which part of the process is causing the problem. I use the same equipment to make quantities of vegetable soup that I can freeze. Also humous from ground chickpeas. Both have plenty of chillies and other tasty ingredients for variety.
This is all normal for me. The trick is to make large volumes and freeze it. I still get a variety of side effects from coffee but I think that they are due to things in the coffee itself but I enjoy a cup at the weekend and put up with the consequences.
Hope this gives you some ideas!