He's not holding a grudge he's scared of you. We are always teaching more than one thing when we are teaching something. You may have taught him potty training, but you also taught him fear. Submissive peeing and poop eating has been linked to overly aggressive punishment in potty training. It really important to understand the basics of potty training before you bring home the dog, and this is something a good breeder would have taught you. Aversive punishment does work in modifying behavior, but there is always some side effect and the side effect is usually fear, which can lead to aggression. I try to advise new pet owners that their first job is to teach the puppy a feeling of safety and comfort. Your hands should always be seen as something good not bad. Potty training takes consistency and patience reward the success and ignore the mistakes.
Some of the others might have suggestions on how to help your pup. The only thing I can think of is to try and teach your puppy that your hands are good. Have you thought about a puppy training class, it sounds like you need to learn lots of basics. I personally don't think yelling should ever be used, and when training as few words as possible should be used. You might try carrying around a small bag of cheerios, and go to another room and call the dog, when he comes reward him with a cheerio. I do a lot of training with Joey, he's not the type that loves to be held for hours, but he does like to play fetch and perform tricks, I think that the time we spend training is very good for him, and he seems to enjoy it, but if you find yourself getting frustrated, they will sense this, so you need to calm down. When grooming you dog, be gentle and reward for good behavior. It's more important that they learn to enjoy grooming than be perfectly groomed at first. I think it might help you if you read up on submissive urination.
Behavior: Understanding and Modifying