We brought home a 1 year old mini-daschund about 2 months ago. He is great, but about 2 days ago he started scratching his ears and rubbing them on the carpet and whining. I have cleaned the edges out with Q-tips and was able to clean out some brown gunk, but although he was very still, I was afraid to clean too deeply and risk damaging his ears. He also has developed some thick places at the base of his ears and his losing some of his hair in those places. I do not know if this is related or not. We have not taken him to the vet yet because his shots were all current when we brought him home. Any advice would be helpful.

It sounds like an ear infection. Some antibiotics from the vet should clear it up. May as well have a heartworm check done too, and start him on a preventative now, before the mosquitoes come out.

Vets have very effective flea treatments too, but you could try some of the over the counter monthly drops or creams.