Did the system operate correctly before you changed the lines and filter?
Are all of the loader functions slow and jerky?
If you operate the tractor at lower RPM does the system smooth out?
If answer to the questions above is yes I would suspect new filter is the problem.
Strainer would be located inside the reservoir on most tractors transmission case. I would suggest following the inlet line back to where it connects to the transmission housing. On some tractors there a cover that you remove to access the strainer in that location.