Why is the booster fan pulling cold air from outside

Sometimes it is necessary to adjust the fins on the downstairs vents to restrict some of the airflow so that more will make it to the upper level. This is especially true in cases where there are no dampers in the ducts of the type described by BMitch in his answer.

I have a similar problem in my own two level house where I have to adjust the vent fins two times per year to set the proper upper / lower level air flow.

Another important question for you.

Have you checked the primary furnace air filter to make sure it is clean? If this has never been changed it could be restricting the air flow design of the whole heating/cooling system. I've seen these filters so clogged up with dirt and dust that it was a wonder that the furnace fan was able to circulate any air at all!!

All the things you've done should have helped some, except the duct boosters. They can't add much flow to the system unless the return ducts were increased proportionally (or similarly boosted). You get increased flow by increased pressure or larger ducting. Keeping upstairs doors closed will help by slowing the 'fall' of cooler air downstairs. Try leaving fan "ON" for a 24 hr period to see if your house will equalize better.

You can force the system to concentrate on the upstairs by reducing both the supply and return vents in the main floor and basement. You may have to do some makeshift blocking (reduction ) of the returns with plastic sheeting and 'no residue' duct tape. If successful, I believe magnetic covers are available.

AFA blocking above the upstairs ducts, by all means. Save yourself some expense (and trouble, that much foam is hard to scaffold in a vertical shaft) and make 2x4 blocking (essentially fire blocking) to go above the vents. If you have typical framing 16 inches on center, a 14 1/2 inch piece will span stud-to-stud. Use a pair of pocket screws on each end to secure the blocking in place. Use fire caulk/foam for any gaps.