I run a -2 inch on my banshee with a stock shock and an adjustable lowering link. It works awesome in the corners but can get a little sketchy on the starts if you don't slip the clutch enough.
If you removed the shift forks from the shafts you may have mixed them up putting it back together. This will prevent you from being able to seat the transmission shafts in the cases.
Those look like older Lonestar racing a arms. I have lsr on my yfz450 they have that same logo.
this is a pic from ebay of a lsr steering stem. look at the logo on the key switch plate.
something about that seems off. when searched through partzilla I come up with
https://www.partzilla.com/product/yamaha/3GG-85510-01-00?ref=9d077fe5f70ab4305de8d5fc6f798023ed59f9a4