It seems that here the answer to every problem is that the scanner is at fault...
I have the 124G as well, and I don't even attempt to focus without using the magnifier. My eyes just aren't what they used to be. So if you're not using the magnifier, I'd say suspect #1 is user error.
During your cleaning, did you remover the ground glass? If you did, did you put it back correctly (smooth side up)? Looking at the full sized image, it looks like it's slightly back-focused. Was your son's eyes your point of focus?
Did you focus and re-compose? That could slightly throw off focus, but (usually) dof takes care of this.
As said before, Taking and Viewing lenses may be out of calibration/synch. Have fun with that if that's what it is.
Subject movement (your son) after you focused but before you hit the shutter may be a cause. But, camera movement/shake is not what you have here. A tripod wouldn't have made a difference here. Besides, would the 124 series have been so popular if it needed a tripod everywhere? Nothing I can see in the image has the look of camera shake/movement. If someone sees it, please point it out to me.
YES, there are an equal number of possible causes directly related to your scanning, but that can not be discussed here....
The below photo was done at a little further distance then yours (about 20-25 feet I'd guess), hand-held. Film was Arista EDU 100ASA, shutter speed and f-stop I don't remember, but it was definitely slower than 1/250, possibly lower than 1/125. F stop was most likely in the f/3.5-5.6 range. Scanned (Gasp!!!) on a Canon 9000II F at 2400 dpi (or maybe 1200 dpi). The crop is at 100% of my daughter's eyes, and I think it's closer to what you were expecting from yours.
If I were you, I'd probably burn a roll doing nothing but focus tests. Hang a newspaper (an ancient news distributing system used before the internet, but after town criers, and still available at your local convenience store), and do the test mentioned above. I'd probably do it both with the magnifier and without, as somewhat of an eye test. Really scrutinize the negatives with a loupe/lens, and compare what you see through the loupe with what you see on you computer screen after scanning.