That was probably a little too much in one go for a puppy. Puppies learn natural dog behavior from their mothers and rudimentary human behavior from their mother's owners (that's called socializing). They are most trusting and confident in situations they experienced in a positive way during socializing. Everything above and beyond makes them insecure untill they learned how to cope with the new situation.
After such a negative experience, you need to give your puppy much love and, if possible at all, repeat the same or a similar situation in a much more positive way.
First there was cutting the nails. This is not an activity you usually do with a puppy during socialization and holding the feet of a dog is not part of the natural behavior. Almost all dogs get nervous during nail cutting at first and need to be trained to endure the procedure in a calm way.
You should train "holding hands" with your puppy. He can be sitting up or lying on his side (to hold the feet). Just pet him a little, take one of his feet in your hand, look at it and move it a little bit for 5 - 10 seconds, then release it and continnue petting. This connects the experience with positive emotions.
Next you should include the nail clipper in this training. Let your dog sniff at it, then do the "holding hands" training but instead of just holding his feet, touch his nails with the clipper. You don't need to actually clip his nails, just touching is enough. Continnue petting after that.
Next time you need to cut his nails, repeat the same training, this time actually cutting his nails. Pet him after every single nail that was cut.
Next the bath. Many dogs are afraid of the bathtub because they cannot see the shape of the surface clearly, it makes a metallic sound that most dogs aren't used to and amplifies sounds and on top of that, they get wet. You could compare the experience with a ghost train for dogs.
Some simple tips to make the experience less frightening are:
- A very simple solution is to put an old towel or bath mat into the tub, to dampen the metallic sound and make it easier to discern the bottom from the walls.
- Kneel down next to the tub so you don't tower over your dog (which is perceived as a dominant or threatening gesture).
- Start the water at low water pressure and let your dog sniff / lick at it.
- Start wetting his feet, then tummy, then shoulders and hips.
- Do not let water flow over his head or ears. If he's dirty there, cup water in your hand and wash him that way.
- Talk to your dog and praise him.
Always use a shampoo designed for dogs. Shampoo for humans shouldn't be ingested, can dry out a dog's skin for several weeks and cause itching or rashes.
Once you're done, either let your dog jump out of the tub or lift him out. Offer a towel in your open hands and call him to you. Rub him dry in a playful manner. Our dog loves to rub himself on the towel and squirm around on it.
Last but not least, the ears. I share your fate in that regard. Any ear infection is extremely unpleasant for a dog, and so is getting any liquid into their ears. Our own dog whines as if he's being slaughtered every time we treat his ears.
Don't grab your dog by the snout and force his head into the position you'd like. Don't clamp his head between your legs. This is not only a form of violence, it also means a rather severe punishment in a dog's natural body language. That way you connect treating his ears with very negative emotions and he will fight harder and harder against it.
Instead, you need to have more patience and outsmart him
You should start massaging his ears with your non-dominant hand. In case of an infection, it's best to massage from the cheek (inner ear) towards the neck (outer ear) to dislodge any acummulation of ear wax. If there is excessive ear wax, it's best to wipe it out with a moistened cotton swap before applying any medication. Do not use Qtips / cotton buds in a dog's ear.
Then move your dominant hand (holding the medication bottle / dispenser) to the same ear and quickly squirt some of the medication in the ear. Continnue massaging the ear to spread the medication. If the medication is very liquid, you don't even have to aim. It'll flow into the ear while you massage. If it's more like a gel and your dog won't let you aim in his ear, squirt a dose onto your finger tip and gently push the finger as deep into the ear as you can get, then massage. Be carefull not to hurt your dog with your finger nails.
After each treatment, give him some very special treats he doesn't get every day and praise him.