My spark plug seems to clearly indicate that my bike is running lean, but whenever I try to richen it up it runs worse.

The motor is stock and I replaced the crank seals when I was getting it running. It does leak from the clutch arm seal. I swapped out the points for an electronic ignition from Rex's Speed Shop.

The needle is on it's lowest setting (clip in the top groove) and it runs pretty good! Revving the motor, idle, and mid-throttle all are really good. (Especially once it's warmed up) It will stutter a bit at nearly full throttle a bit.

Raising the needle one step makes the mid-throttle response stutter and the bike loses some top-end power.

Our altitude here is ~5000ft, so I had thought that it needed to be leaned out because of that. However, after driving it a bit and looking at the plug I'm concerned that I'm going to ruin the motor.

Plug picture

So... what exactly are you worried about? Not sure how you took your plug reading but the one in you picture certainly doesn't look lean... unless I'm missing something?

(Tried to insert your plug picture into this post... not sure if it will work, never tried it before.)

Plug look fine to me. I'd be happy with that coloring. Remember the needle is only changing mid-throttle to WOT. At your elevation, I would probably re-jet so that I could get the needle back to the mid-point so I could fine tune from there. At the top spot, you're stuck.

Thanks for the feedback! I was using the plug pictures/guide on this Mikuni tuning page, and it seemed like it might be lean.
www.vintagebikebuilder.com/mikuni-tuning-and-jetting-guide.html

It's been on my mind to order the leaner jets/parts, but I need to figure out what's in it. (I'm pretty sure it's whatever came with the bike, nothing else has been modified on the bike and it was in California, so likely closer to sea level.)