You cannot combine the booking numbers. You have to check in separately. This also means boarding separately. But the first person to board can save a seat. We are usually only a few numbers apart, but we checking as early as possible.

Once you add your companion ticket to an already booked ticket you end up with 2 booking numbers. Has anyone had success combining those booking numbers to make check-in more convenient

You do have the concept right, but your numbers are a bit confused.

You get 60,000 sign-up bonus, + 40,000 sign-up bonus, + at least 4000 points from meeting the minimum $4000 spend to get the bonuses. That equals 104,000 miles/points.

Then you need to earn another 6000 points (through card spending, flying SW, care rentals, etc.).

Once you hit 110,000 miles/points total in a calendar year you get the companion pass, plus you still have those 110,000 miles to use to purchase tickets.