Okay I feel your pain and most of us have been in yours shoes with similar things, toilet training, puppy blues etc. Doesn't matter how much you think you're ready, nothing can prepare you for the often awfulness of puppies. Pineapplepup is currently doing zoomies around the room and just generally being a complete pain in the arse, it's the witching hour and I hate it!
Forget leaving pup on his own for a while, it'll be quite some time, where you go, take him with you, it's easier.
I work from home too, I've moved my office to the kitchen table so pup can play/sleep and I'm right next to the door to let her out into the garden a million times a day.
Routine is your friend, Pineapplepup wakes up (in her crate) at around 7 everyday. She wakes me up by yapping at me (she's in the room next to mine that is usually my office) and I open the crate and she goes straight downstairs and out for a pee and a poo (with me obvs, she hasn't mastered opening doors yet) Then breakfast and playing for an hour and a half and then back to her crate so I can shower and start work. On a good day she'll sleep through to gone 12 giving me a few hours peace. On wake up, straight out for toilet again and then more playing whilst I work. Then out for a walk (thats still a work in progress) for half an hour. Then lunch and more playing, interspersed with peanut butter licky mats, treat snuffling and lots of chewing on yak and pizzle sticks, she's a big chewer. Then comes witching hour , her dinner and then she very carefully watches me eat dinner and then tends to settle down for the evening, maybe a bit of playing with her toys before going out for a bedtime wee and up to bed at 10 (or slightly later depending on when I'm a celeb finishes) she goes straight to sleep and sleeps through til morning.
It's hard work (especially as it's just me and her, no one else) but she's 16 weeks tomorrow and we almost have toilet training licked, any accidents now are my fault for not letting her out quick enough and all the accidents are on the hard floor next to the french doors so she was near as dammit in the garden! She also slightly less bitey and slightly more calm. LOTS to work on but she's come a long way in the 8 weeks I've had her.
I think you're brave getting a puppy with cats, I waited until my cat had passed away before I got the puppy, no way would my lovey cat have put up with a puppy!
Accept your life will be quite different for a while and some other things in your life will have to suffer/pause for a bit, they aren't puppies for long, as most of have said at some point, this too shall pass.