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I am one of the brave souls that trained both for pads and outdoors, and it can be done, it takes a bit more work and Gucci still thinks bathroom rugs or door mats are fair game when it comes to potty'ing, although..I may have outsmarted her by putting her pad over the bath rug, lol
Seriously, though..she would often 'miss' the pad in the early days. I suggest getting some old vinyl remnant / tablecloth, a cheap one at the dollar store or Walmart and cutting it in half and putting it under the pad, until he gets the hang of it a bit better.
As far as barking at 5am, I'm not sure on that one. Gucci sleeps in bed with us and she's content to know I am right there with her.. and just gets up whenever I do..so I'm pretty fortunate in that regard, I am NOT a 5am sort of person. Either he wants to go potty and his bladder will eventually grow and get stronger and he'll be able to make it til' 6 am, or he wakes up and he wants to see you
One thing I found challenging as for as pad training is that she didn't like to poo where she went pee. If I had figured this out early on, it would've saved me a few months of scratching my head, lol.. Of course it would be easier if they could tell us these things, but puppies aren't all easy, I guess that's why they make them so darn cute.