Bravo Gabriel!
I mainly just wanted to say what a fine thing I think you are doing. Any kind of First Big Bike will likely be a cherished memory for the rest of the kid's life.
My only advice would be to keep any bike reduced to as simple as possible, so there is less to go wrong or jam up and discourage the kid.
Nothing wrong with stem shifters. So long as they are checked out and properly adjusted they will be a pleasant non-threatening way for the boy to learn friction shifting. I picked up an old Peugeot from a local thrift store (for a charity donation project) which had long stem mounted Huret friction levers and I was truly amazed at how well they worked. I'd never had them on any of my bikes back in the day, and assumed they were terrible; I was wrong.
Although "we" may agonize over correctness for our own cherished restorations and spend obscene amounts of money on them to that end, we often lose sight of how little it really takes to put a neglected but serviceable old bike back into tip-top running condition. New cables, housings, brake pads, a fair investment of time to dis-assemble, examine and re-lube everything, and a decent old workhorse bike will quite often be rolling along merrily, once again. I doubt that will be true of the modern, more complex, bikes sold today; imagine the thrift store bike of the future... one with a busted STI mechanism.
Good Luck!
"Get a bicycle. You will not regret it, if you live." ~ Mark Twain
Bob Hanson, Albuquerque, New Mexico, USA