Hopefully the last of my initial problems. The bike frequently has trouble shifting from 1st to 2nd. Sometimes it will shift smoothly but most of the time it doesn't shift or it shifts into N . Any ideas why this must be happening?

This is on my 2003 Superglide Sport FXDX if my signature isn't showing up- I just tried the mobile site

 

It being a older bike I would check small things first.
Check the linkage going to the transmission. Take one of the bolts out and check to see if it is stiff. If it doesn't have a hem joint I suggest adding them. While it is disconnected check the shifter for tightness, looseness etc... Make sure the shifter is tight on the shaft.
I would still lube all serviceable parts. If it is still not shifting right. Change to a good tranny fluid of your choice. I use Amsoil severe lube 70-90.

 

Check your clutch adjustment. Harley trans love synthetic oil - makes them shift smoother and reduces gear noise.