Some of the rafters and floor joists were perpendicular to the walls and crossed into both spaces. 

The direction of the joists determine how it gets bolted as well - if the joists are perpendicular, you have to install scabs and also run the scabs back a few joists to account for roll-over. 

My thinking is if you fix the wet basement you could run wood or laminate flooring perpendicular to the floor on there now.

The stud is a vertical 2X4, maybe a 2X6 board inside the wall, you should cut one like it and place it in so that it acts as one piece running vertically and then use some lumber to scab on to the sides of the joints, placing a new piece on the side of the stud where the joints are.After that, you might use 2X4s perpendicular to the floor between the stud repaired and the corner stud.

Place the base on edge and scab on the side to the rafter, at a 45 degree slope and nail to the rafter, the base is running perpendicular to the rafter and ceiling joists.

The plat showed a 90 degree turn, and straight streets, and property lines perpendicular to the street.

There are two attics (The addition has a roof that runs perpendicular to the original, and for whatever reason they did not tie the two spaces together.

From your experiences, have you noticed any major differences between properties where grass is perpendicular to the foundation pier versus cement?

That will depend on the condition of the decking as well and there are perlins under the metal (or should be) boards running perpendicular to the roof for the metal to be attached to, so the condition of that decking surface may be an issue, won't know until it comes off.You might inquire about a roof over, where a new roof is place over the old rook without removing the old roof.

I'm sorry, Jon, but it sounds an awful lot like you're asking us how to draw seven red lines, all of them strictly perpendicular, some with green ink, some with transparent ink.To clarify, not the task, but the general sense of how this is being asked, do you want to retain the right to get rid of the tenant in the winter months for nonpayment of rent, egregious lease violations, your decision not to renew, etc.?