Started to work on a Habitat for Humanity house.  It will be a duplex, basement with two floors above; the roof will be an six pitch with gabels.

While trying to put down subfloor on second floor, I noticed that many of the LVLs and I joists were not even,  Some LVLs(11 7/8″) were 3/8′ above some I joists while other I joists were 1/4″ below the LVLs.  The flooring did not lay even one the I joists.  

How to fix so the floor will lay even and not bounce in the future.  Thanks