Here are my answers. Others may have different opinions.
So my first question is, this is a Commander II 130/90 B, did something go wrong with the tire such as belts or balance, or is it just because of how many miles it has on it?
I think that 25,000 miles is pretty good, even for a front tire. It could be just the tire worn out causing it to shake. Run your hand along the edge of the tread and see if you feel any cupping. The other possibility is that the steering head bearings need tightened and probably greased.
My second question is, I have read and would like to try the Elite 3's. I have seen what size to get for back. What size did you get for the front? All I see is a 150/80. How much difference is there going from a 90 to an 80? Would this have an adverse affect on the leveling links?
150/80 is the correct tire size for the front. Not sure where you are coming up with the 150/90 number.
Third and final question is about the leveling links. I am interested in them and would like to try them. Where do I get them? I have looked on Diamond R Accessories page and don't see them.
You might check with member Carbon_One here on the forum. I got my last set from him. I tagged him in this post so hopefully he will reply.