the bolts with the ground there are because the stock signals ground thru their body so you would need them. with your aftermarket ones they will have a ground wire, most likely at least so now the old grounds are superfluous
You can use a three prong flasher it just has a dedicated ground wire and you would have to ground that in order to use it. grey goes to one terminal, black to another with the two prong and if you use a third the ground lug
Just remember that the way you are gonna run your turn signals up front that it supports your headlight now so you want a nice solid mount so it isn't buzzy
If you mean the turn signals themselves have three wires then you have front running lights. You connect the running light function to the orange/white and blue/white that comes from the handlebars. The regular turn signal lights go to solid light blue and solid orange and then ground those suckers. You will prob have the extra ground spots in the bucket at one of those junctions