1. You can get a decent entry level mtb in your budget, so keep that in mind for later.
2. Saddles are highly personal and generally takes a lot of trial and error- it's one of the first things most people swap out. Consider going to a Specialized shop and have your sit bones measured. Also keep in mind the width of the saddle depends on the riding posture- the more upright, the wider the saddle needs to be. Just don't get one of those big arsed, gel filled tractor seats.
3. Handlebars- stay away from carbon. Steel can rust if precautions aren't taken.
4. Grips- use the stock ones for now, but get some gloves. Gloves save your hands from road rash in case of a spill. But if you do swap out grips, make sure you get some that lock on. I personally use Ergon GP-1's. They allow me to use whatever bar ends or a mirror that I want.
5. EMS sounds like they just want to sell you what they have and not necessarily what you want; as they aren't the only shops in town, I wouldn't bother going back to them for anything if I was you.

Also note about handlebars- one is that flat ones can be cut down a bit if they are too wide. I'd say ride them for a bit, then move the grips and controls in a bit a little at a time until you find your sweet spot- then either cut 'em yourself or take it back to the LBS and pay them to do it for you. Secondly, swapping out from the moustache to a flat bar may require swapping out the stem as well. Might see if they have an adjustable stem that you could use to figure out height/reach, then swap out to a solid stem that replicates as closely as possible.