Hi Rhi
Thanks very much for your praise, glad you found the site useful, it encourages me to get on and get the site finished.
You're not the only one with very shy chipmunks, given you've had your for a few months now I think you can say they have got settled in. I think the boys hiding in the nest will get used to you, but I find it can take ages. My chipmunk Izzy would run and hide from me every time I came in the room. He's a year old now, and last week he actually jumped on my shoulder, not for long though. What helped tame him this far was him being let out, he's one of two I've got which are painfully shy. Tucker is my other one, he was spending nearly all day in his nest box, but now he will come out and watch from a shelf in his aviary. He is going to be hard work as he shows no interest in wanting to come out for a run.
Having three boys could be a problem in the future you may need to separate them as they get older. I really thought that brothers from the same litter would be OK, but not always. All my male chipmunks need to be watched when they are in the same room running around, and all of them have to have their own aviaries. If left alone and together, there would be a fight, which can be fatal. The only exception I had was Pickles and his brother Arthur, who could tolerate each other. It will be interesting to see what happens with your three boys, it could make a difference that you don't have any females. No females could mean they won't be so territorial with each other.