This Im afraid is your quadracer now  The difference between a novice and an attentive mechanical mind is worlds apart. goodluck< and let us know if you dont get it sorted.

Sounds like the hub bearing is not seated in all the way. an easy way to check that is to feel the bearing spacer and check if it seems sandwiched fully. I believe if you crank the spindle nut tight it should theoretically pull the bearings together squishing the spacer in tight and seat everything fully. correct?

Your factory calipers have two pionts that slide, side to side a bit. One is the piston. the second is the sliding bolts. The yfz450 calipers are the same technology/design but with dual pistons> not to be confused with opposing piston calipers wich have to work around different design and function. By the way those brakes your working with now are the identical design to 90% of the brakes on the road today.