Ugly Ground!

"It is 2018. The U.S. Government has taken control of all major airports due to a drastic rise in airline crashes ,unheard of airfares and 60% cancelled flights. During this takeover, the Government has decided to rebuild the airline infurstructure in the U.S"

With this scenario, I have set out to "rebuild", from the ground up, all major airports in the U.S. To date, I have completed KJFK, KPHL and KATL. I had to stop due to a lack of knowledge on the MSFS ground mesh. When I move runways and taxyways, most, like KATL leave an original footpirint that is ugly as the dickens! When I use AFCAD or ABACUS ground cover to cover up this unsightly mess, my frame rates plumet!

My question is: What can I add/do/adjust to clean up the original "footprint" and save frame rates?