Trying to crate train in an apartment while working from home

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I have a 13 week old mixed breed boy (we think lab / boxer / heeler) that I actually whelped here at the apartment and he is finally coming to the age where I feel comfortable beginning training. I probably should have started earlier but this is all a new process for me and I wasnt sure when was right.

Previously, we were allowing free roam with puppy pad training since I worked from home and we dont have a private yard to allow him to go outside. We're now learning the hard lesson of separation anxiety and we want to nip it in the bud NOW.

The good news is that he's slept in his kennel at night since he was born, so he's accustomed to going in there for bedtime. We still have to lure him with treats and he doesnt respond to "kennel up" yet, but he doesnt whine through the night and usually goes to sleep within a few minutes. The trouble now is daytime crating.

The current plan is to kennel him in the bedroom while I work out in the living room. I'll be there but with the door closed and the TV on, so he shouldn't know it. Today (day 1 of this new plan), we got up at 7 with him, pottied on the mat, ate breakfast, and then played until 9. Then we put him in the kennel from 9-12. For lunch, I took him out for another 2 hours for potty, food, and more play. He then went back into the kennel for another three hours (2-5) and is then let out to free roam with supervision for the evening until bedtime (midnight).

My biggest questions are thus –

Is it inadvisable that I stay near the kennel in these first few days? He screamed for quite a while before I opened the door to let him know I was in the other room. I gave gentle shushes and no nos when he'd start crying again and he would stop, but I'm afraid me being within eyesight will defeat the purpose of trying to separate.

He can't go outside to a public yard for another 3 weeks or so. He's only had 2 rounds of parvo vaccinations. How big of a risk am I running if a allow him to go on my porch for potty time? I'm really trying to get rid of the puppy pads since I know this encourages them to go on soft things but I dont know how dangerous it would be and don't want him hurt of course. Theres a dog potty area nearby but theres only about 5 regular dogs that cross my door yard through the days.

Mildly unrelated – He HATES the harness and collar still. Do I just need to keep exposing him to it or is it still too early? I guess ultimately I'm unsure how to go about pottying and crating the most efficiently while I'm here constantly.

Any advice would be greatly appreciated!

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