I would paint the metal rod (after priming it first), them mask it w a piece of Post-it cut to the right width. Parafilm M is also good stuff for this. I can't tell how big the model is from the instructions; if it's really small, I'd just brush paint it...
If the end result is imperfect, it's easy to touch up w/ a brush, and carefully applied washes will hide small imperfections. I use a subtle wash of Black mixed w/ Burnt Umber to replicate lubricant stains and hydraulic fluid leaks.
PLU1 is right about the Flex-I-File. That's exactly what I would use to clean the seam. Those things are awesome. Cheap too.
I first put Tamiya liquid cement on both surfaces to be mated, then I run some more into the join just before I press it completely closed. I rarely have too many problems w/ seam cleanup.
Even if you don't get it perfect, how visible is the seam? My friend Henry says: "If it's not visible, it not a mistake."