Kubota removed the "Build my Kubota" pricing configuration tool from it's website on July 1. I had been looking at the M9540HD before July 1 and the price was $34,317. The price for the M9540HDC was $41,809. Loader prices vary because there are several options, which size bucket, 3rd function valve, kubota shockless ride, self leveling, etc. I think the list price on a loader and bucket will be around $6700. I'm not sure about the radial tire option, and if it comes with the standard steel wheels or if it includes the cast iron rear wheel centers. I would just guess that it would list for about $1500.
So, for the M9540HDC ($41,809) plus loader ($6700) plus radials ($1500) you get a list price of approximately $50,009. I think the M8540 price was about $2400 less than the M9540, so subtract that to get about $47,609. A price of $41,000 is approximately 16% below list price, which is pretty decent.
Kubota rebates on M series went from $600 down to $500 on July 1, and the financing terms got slightly worse as well.
Please keep in mind that this analysis includes a couple of guesses/estimates/assumptions, but I think it's fairly close. Hope this helps.