If the bike ( 2005 yz 250f ) starts right up and seems to run just fine, How do you know when it needs a topend rebuild? When I kick it over it does not feel like it has the same compression that my 2002 yz 250f does. Any advice

if the valves are in spec then a compression test would be the best indicator.....

Without a compression tester, a down and dirty way to check the compression is to use your thumb. No matter how hard you hold your thumb over the spark plug hole, the compression should push it off.