Just purchased P-51 Mustang PTS. Came with cockpit master simulator. Is there another software that will work with my JR (XF421) transmitter.

You can buy an interface cable and download FREE FMS software heres the cablehttp://cgi.ebay.com/RC-Simulator-JR-FMS-Cable-wBouns-Aircraft-NEW_W0QQitemZ6008066033QQcategoryZ19164QQrdZ1QQcmd ZViewItem
EDIT: the link didn't work. Go to ebay and search FMS you'll get it

Is it better than what came with the plane.

I have no experience with either BUT alot of people on here talk about it. SOmeone with experience will chime in here soon I'm sure

Bear in mind that the flight sims will give you an idea of how the plane will react in relation to the stick movements. ie. If you pull the right stick toward you provided the plane isn't inverted the plane will climb. The sim is not to be used as a substitue for an instructor with a buddy box. There is no way a small puter screen can look the same as the field. Ground handling is also very easy on the sims as compared to a real grass field. [8D]The more expensive sims have better looking graphics but the planes still handle basically the same.

If you are looking for a better simulator and you are willing to spend a bit of money i would recomend aerofly professional deluxe or real flite G3 there are plenty of pictures of screenshots and videos of these sims here on rcu