I definitely support you in testing for nightshades and bet you'll see a result, but I would also ask you how often you eat sauerkraut and if you've ever reacted to it before? I remember reading recently (pretty sure it was in Practical Paleo, but not 100% certain) that fermenting already goitrogenic vegetables actually increases goitrogen content. So the kraut that is awesome for everyone else is not so awesome for people with thyroid conditions. Personally, I thought it was great for me, until I went several weeks without it and ate a bunch and my throat swelled up.
Your diagnosis sounds worthy of testing by eliminating nightshades.
Here is a good list... http://www.whfoods.com/genpage.php?tname=george&dbid=62
Here is a nice discussion of good substitutes for nightshades... http://www.livestrong.com/article/265055-list-of-foods-for-those-allergic-to-nightshade/