I replaced the top end of my 1999 yz400f. got it to start but it won't stay running unless the choke is on half way.

The most common answer you will receive for this question is more than likely check and clean your pilot jet and pilot circuit with compressed air and new pilot jet ideally. I must confess in most cases this does apply except the last 3 rebuilds I have done on 400, 426 and a 450 YZ exactly the same problem where hard to start and when started only wanted to run with choke on they all ended up being leaking intake valves
Best option if you can is clean pilot circuit replace pilot jet - Then double check your valve clearances (sometimes to tight can leave the intake valves hanging open when meant to be closed) then if still no joy, Do a leak down test or get your local shop to do leak down test - The leak down test will save you a lot of frustration diagnosing internal issues. Just to clarify don't pay too much attention to the percentage loss of the test just do the test to confirm if there is a leak or not.
good luck - Regards Jamie