I just wanted to welcome you to Yorkie Talk too!
I agree it sure sounds like you're doing an awesome job with clipping your new baby boy's nails and caring for him. There is no harm at all in trimming his private parts and this may very well help keep him cleaner.
I only have girls so I'm sure not an expert on boy yorkies although I'm sure there will be some other members on here that can help you out in that area. I know there is definitely no problem with him getting an infection if you keep him clean, in fact it could actually prevent one.
If you're shaving his ears in the next few days then I'll tell you what I do with my girls. I use a mustache trimmer and trim the top third of the ear tip only front and back and then use my rounded scissors to trim around the the tip of the ears to clean them up a bit. This helps keep the ears looking really perky and clean and prevents from drooping when the puppies are still quite young.
Good luck with all of that! It sounds like you've already got a handle on this but hope it goes well for you!