I have a 92 lt250R Quadracer, that I just rebuilt the top end on, while it was apart I checked the rod big end for up&down play and had none. After about 1 hour of break in time, with the engine running great I notice a clicking noise coming from inside the motor, when it is idling.

Any insight would be helpful.

 

You ned to isolate the noise first. With the tip of a long screwdriver (plastic hadle) touch different parts of the engine with your ear to the handle. This will transmit the sound to your ear like a stethascope. Find where it's the loudest.
On old engines, it's not uncommon for a bottom end that seemed fine to pick up a nock after the top-end has been redone. Putting compression back to spec or better can over stress the old big-end bearings very fast. It could be other stuff also, so find out for sure where it's comming from.