Friend, it sounds like he may have a skin infection in the inner skin of the pinnae. This is what you can do:
1- Wash the skin with an antibacterial soap. Then, apply a topical antibiotic like neosporin or bacitracin. Do this 2 times a day for the next 7-10 days.
2- To clean the external canal, mix in a cup 1/3 of white vinegar with 2/3 warm water; use this as an ear cleaning solution with cotton to remove all of the ear wax.
3- As far as the bumps on the skin, in a puppy, common causes are insect bites, infections, allergic dermatitis, etc. I would bath him with chlorhexiderm shampoo 2-3 times a week for 2 weeks. You can buy chlorhexiderm in your local pet store, online, etc.
4- If no improvement after doing the above follow up with your family veterinarian for a hands-on examination. If cost is a concerned look into your local ASPCA or Shelter where they often offer veterinary services at a lower cost.
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