Usually guineas will stick around their home turf, but it sounds like yours didn't have enough time to get used to their new enclosure. And they are tough to catch!
Do you have any smaller wire cages where you could put the three birds in your lean to? If you do, put them inside and keep the cages in the lean to. Then open the door to the lean to but be sure to have food and water inside. Make yourself scarce, and come back in an hour or two and see if the strays have returned. If they have, close the door, and you are good.
The other option is to just keep a watch out and see if you can figure out where the strays are roosting. If it is not too high, it may be easier to catch them that way once they go to bed for the night.
Were you planning on free ranging your guineas once they are acclimated to the lean to? If so, then you might not have to do anything beyond putting food and water out for the strays. They may stay close by to the three in the lean to.