If that company is not affiliated in any way to Canada or Canadian clients, no issue in regard to PR application as long as you don't claim any points for that.
It's not a misrepresentation, it's your call to be accompanying or not.
Letter of explanation is not required, but won't do any harm and may be useful if written concisely and to the point.
Add your husband as non-accompanying. Get his papers ready and change to accompanying. Then you will be requested to submit all his papers.
But make sure your calculations are correct.
You can try as many times as you need.
No it does't count as express entry application. Application is when you get invitation to apply and you submit your actual application.
Well it happens. Sometimes those requests come back in 6 months and more. Just apply again. These requests are not on the first come first served basis, so reapplying helps.