Ok so my Yamaha is being built to be used as a trail riding bike. So I was wondering do I need lights on the bike or should I just leave them off? Also there seem to be a million different handlebars and grips. How do I choose which ones to use? And finally should I leave the front fender stock or get one which mounts higher?
You may want a light for night riding. Open field, plus snow, plus night equals awesome times.
keep a minimum head and taillight. never know when you'll want it on a fireroad or two.
bars & grips? Try Renthal bars with whatever grips feel right
how much mud you gonna play in?
Refresh my memory, exactly what kind of Yammie are we dealing with? Never mind, I went and looked at your other thread. I eventually figure things out. 
Headlight and taillight are great for getting back to the truck when the sun goes down and also for being seen by other trail riders.
Low mount fenders work everywhere but mud. Sticky mud will get packed on the tire and then jam into the fender, not good.
Bars and grips are a personal thing. I always preferred Renthal 'Button Bend' bars, tall and pretty straight compared to a lot of others. 'CR Hi' bends were close but not quite as straight. But that was on bikes I spent a lot of time standing up on, you may find something completely different works for you. I will say that 95% of the stock bars out there have too much 'sweep', they forced my wrists into a real unnatural position. Sometimes all you need is the stock bar height but then use a real long piece of pipe to bend the bars more straight. But from the pics I'm going to say you will probably need a taller bar. When you need to stand up (essential in off road riding), if the bars force you to squat or to bend over, your knees and back will be screaming shortly.
Something I was shown many moons ago: put the bike on a stand, sit on the bike in a natural position with your hands at your sides. Then close your eyes and raise your hands like you are grabbing the bars, get your hands into a comfortable spot and then open your eyes. Where your hands wind up is the type of bar bend and width you will be most comfortable with. Bar height is determined by standing and seeing what makes you comfortable.
Sometimes it's not even the bars. A common trick on XR400 Hondas was a set of 'Bar Backs' which were aluminum blocks that bolted to the stock bar mounts but moved the bars forward about 1 1/4". Those made all the difference in the world for me.
Grips, there's a zillion of them and it's a personal thing. I loved Gatorz when they were still available, good n' tacky but with a smooth surface so I didn't get blisters. When those went away, the nearest I could find was medium compound 'waffle grips'. I'd stay away from weird shapes (hexagon, the 'bubble' grips, etc) because you just can't get a good comfortable grip. The kind with the tall ribs flex in your hands and make the bike feel vague.
Darn I was hoping everyone would say don't worry about lights since the bike didn't have any with it.
Lights aren't hard to rig. You can grab some from a bike boneyard or use the universal enduro headlights/taillights available from Tucker Rocky etc. You can run them without a battery, but they get real dim at idle particularly on an old scoot like that one. Even that's easy, you can use NiCad batteries to make a battery pack, if you use the little ones you can mount them inside the headlight shell. Snag a voltage regulator at the bike boneyard and you are set.
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