I have read the issue addressed in this fourm not sure if I complelty understood the answer.

When looking at the frame rail I notice a total of 4 holes , there appear to be 2 which are larger
one is at the front of frame rail, the other larger hole is at the rear of frame rail.

There are 2 smaller holes between these 2 larger ones. Looking under my car I see the larger
front hole has a plug, The 2 smaller holes sort of more in the middle of frame rails both have
rubber plugs.

The larger rear hole has no plug, should it have a plug... Thanks

 

These four plug holes are to prevent a wind noise that could occur from under the vehicle. They are usually installed at new car prep. It won't hurt the vehicle not to have these installed.

 

Everything you should need to know about tie-down plugs:

http://www.hmaservice.com/files/331/1299967/06-80-001pdf.pdf