Not sure why it would yellow, did you use any thinners with the clear, you need a high quality thinner in the top coat, you can then clean out with cheap stuff.
Maybe a miss match in the paints.
Basically you can clear straight after you base coat but if you are not 100% confident in your spraying its best to give it half an hour until its firmed off,
this will give good cross bonding in the paint.