First off, great choice on your frame. I bought the exact same one, but it won't ship until Peter is back from Interbike on the 27th.
Secondly, Components. Nothing wrong with Deore XT, but you might want to check into SRAM. It will cost a little more, but after I had a chance to ride a few SRAM bikes, I was sold on the shifting and craftsmanship. If you go to the components thread, you will see one I posted asking comparison between Deore XT and SRAM. Everyone who answered gave great feedback and I have managed to pick out my groupset.
Your fork. If it's in your budget and you plan to ride hard at all, get the best fork you can get your hands on. It's hard to justify a $900 upgrade when you already spent close to $500. If you can, just shell it out now. You will be happier in the end if you ride much at all. Fork performance makes so much difference in the ride you don't want to sacrifice here if possible. Keeping your front wheel in contact with the ground is ever so important on a hardtail. As for brands, I'm only familiar with Fox and Rock Shox. IMO, the Fox Factory 32 series is going to be a little more responsive and supple, but Rock Shox is a little lower maintenance. However, Fox redesigned their air spring system for the 2016 and 2017 models which is supposed to also help reduce maintenance from the previous versions. Either way, go high end here if you can spare the coin. I did. I ordered the Factory 32 Step Cast for mine this past Wednesday.
Now for the Giant bike. Looks like a 24" wheel, correct? If so Suntour has some forks that will fit it. I don't recall the models, but the bottom one is crap. You will want to go min 1 level up. I was looking for a bike for my son over the summer at my LBS. There were 2 used Treks in there. One was a 2014 and another 2015. The 2015 had the nicer fork. Even nicer than the new 2016. It wasn't buttery supple, but it was pretty smooth and adjustable. I think new they are around $200 give or take.
For his components, def go shimano. Just make sure that you stay in the same gear setup or you might have freehub body issues. If you know how to adjust and axle for hub alignment and dish a wheel, then no biggie. It's hard to tell from the pic, but it looks like the BB is possibly a BSA 68/73. This would be a threaded BB. Grab a metric ruler and measure the length of the BB tube from left to right under the bike. If you are exactly 68 or 73mm (not including the cup flanges), chances are that's what you have. It's one of the most common standards and easy to find parts for. You can probably find a standard Deore (M615 I think) groupset pretty cheap. However, I think they are 10 speed. A lot of the Jr bikes are 7 or 8 speed rear. If his is an 8 or more, you may be able to go with a 10 as the cogs are closer together and 8-10 fit on the same free hub body.
Have fun with your new ride. Post pics too. It will be nice to have a few more riders on the MB01 in here as well. :-)