I've read quite a bit about the problems concerning our many fans and their many problems, but am having trouble finding the solution to my problem

every spring on startup my battery has a problem of going dead for the first 2 weeks of driving, I decided this year I was going to see if there was a short or something. So I pulled my fuses and relays one by one to see where the drain was------------there continued to be a drain with everything unplugged. now my battery holds a charge just fine
but, my check engine light came on and I have no interior fan. There is a little bit of air movement (low speed fan?) and the temp. control works, but I can't get any high speed fan adjustment
any direction to look would be most appreciated