Jeff,
It sounds like it's not just the grain alignment, but also the orientation of the clip that's a problem for you. This is likely to only be a problem on fountain pens, as you can rotate rollerballs without a problem! As Gerry said, you can always try one of the three "other" positions for the cap, but that doesn't always guarantee it will line up where comfortable. Try doing what Billy said, but do it for both the closed and open positions. That is, if you've done a pen for which the grain can/should be aligned, you can assemble the cap, then put the threaded portion from the "writing half" of the lower barrel into the cap, align the grain, and then press it together snuggly enough that it's not going to move. Remove the cap, then finish pressing that portion together. If I were you, I'd then install the nib and feeder into the threaded insert you just pressed into the pen, then flip everything around and repeat the process with the threaded insert on the other side, making sure the cap and clip hit your hand in a more comfortable position.
Good luck!