I'm most definitely not an expert, but I am someone who has done something similar with my own son.
Assuming your son is into xc riding, and not downhill/freeride stuff, I'd recommend a nice, middle of the road hardtail frame. You can find lots of gently used medium frames (thinking medium for a 13 yo...maybe small...maybe large) on forums like pinkbike/nsmb and/or ebay.
Going with a used frame will help keep the price down and possibly allow a bit more money to be spent on a fork. Newer 4" travel forks are fairly plentiful, and generally pretty good from manufacturer to manufacturer. As a general rule, I believe there are many good manufacturers for a first fork for a 13 year old....and personal preference often comes in.....I'd recommend looking in the same places as you could look for a frame. You can often find people upgrading their fork.....you just need to make sure the steerer tube is long enough for your frame (and also that the fork is in good shape!).
Remember, caveat emptor prevails when buying used....but great deals are out there to be had.
Good luck! I can't think of a better present for your son than a new bike and the experience of building it with dad!