FYI. You EITHER need another spacer OR you still need to shorten your steerer by about 2mm ...
When you look into the stem without the top cap in place, the top of the steerer should be a 2mm-to-3mm below the top of the stem ...
OR, in those instances where an extra spacer sits atop the stem, there should be 2mm-to-3mm gap between the top of the steerer and the top of the last spacer ...
While the top cap is mostly cosmetic AFTER the fork-and-stem are installed, it needs to be able to snug up the stack AND its edges will subsequently be flush with the top of the stem when properly installed ... the top cap's final "fit" will be the same as if you simply put it atop the stem when it is sittng on a table top.
BECAUSE, if there isn't a gap, then you won't be able to snug up the stack & the fork will wobble within the headset & premature bearing wear will occur + the possibility of eventually damaging the headtube.
IMO, the (¿)easiest(?) way to install a fork (particularly a suspension fork) is when the frame is inverted & the head tube is vertcal ... let gravity assist the installation rather than rely solely on the top cap.
As far as where to locate the brake levers & whether you should shorten the handlebars, that is a matter of personal preference BASED ON the type of terrain you ride on + (to a lesser extent) your upper body strength, etc.
So, I recommend that you start with the brakes & shifters as close to the inner bend as possible & the grips on the uncut bars (this might be stating the obvious -- install the grips with plain WATER ... to remove, you would slightly lift the grip's edge AND THEN drip/seep some water between the grip & handlebars ... wiggle ... continue to add more water until the grip can be wiggled off) ...
Also, PUT a 'coin' whose circumference is the same as the OD of the handlebar on each end of the handlebar ... this is a safety issue which prevents the end of the handlebar from becoming a "plug cutter" in your leg-or-torso in a worse-case-scenario accident ...
AS YOU RIDE IN THE NEXT FEW DAYS/WEEKS/MONTHS, you will find that the brakes-and-shifters are either too far inboard, or eventually just right. Continue to adjust as necessary.
Similarly, you will also find that when your hands are on the grips that you may not be using the outer most portion -- take note of where you are NOT placing your hands, wrap that portion with some tape, ride for a few more days/weeks with the tape in place to confirm that you won't be putting your hands in that wide location ... remove the grips (as described above) & trim the excess amount of handlebar from each side.
Of course, it may only take one-or-two rides to determine the most comfortable lever position & handlebar width which works for YOU ...
I do suggest that you leave the handlebars ~1cm longer on each side than you placed your hands.
The stem length/height will affect comfortable placement & width, too.
BTW. YOU need to buy a FLAT ******* File so that you can 'clean up' the top edge of your steerer + the ends of your handlebars if-and-after you trim them ...
The easiest, IMO, way to ensure a square edge is to wrap the "tube"/whatever with some masking tape ... if the edges of the tape meet when you wrap the object & you "file"-or-cut down to the tape, then the edge will be "square" ... if the edges of the tape don't meet when you wrap the tape, then the resultant edge probably won't be square.
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I'm glad your LBS gave you a store credit.