Background
The raw aluminum panels provided in the Smyth Ute kit can be assembled “as is”. However, there are a number of refinements that enhance both the appearance and robustness of the build. Multiple trial fitments are suggested to determine exactly what needs to be done.
The first task is to drill out all the small pierces to accommodate M8 bolts. The M8 diameter is 0.315″ so a 3/8 drill bit (0.375″) makes a sufficient hole. However, it may be advantageous to drill slightly smaller holes — 11/32 bit or 0.344″ — for a more precise alignment. Note that 5/16 bits (0.313″) are too small.
Under fitment issues you mention the right fender bump. Did you do anything to address this issue?
On our Turbo S, a little tapping with a ball peen hammer removed a slight clearance problem. Bending any intruding metal back should work fine.