I can't seem to get over 650 rpm. Not 675. Would my calculations being wrong on the steps per be the difference?

Calculations there wont affect the max RPM, it is purely kernel speed that will determine that. Steps per will determine the accuracy of the commanded to true though so if you had 2000 steps per rev and you actually need 4000 then your commanded speed would be double the true speed.

What it may be here is that your kernal speed is actually not a true 45KHz due to the computer you have, what does it say the pulserate is on the Diagnostics page, if it says around 43,333 you have your answer as 43,333 x 60 seconds /4000 = 650rpm

Now playing with the numbers in the Spindle Pulley screen: If I put a max speed 1000 then my actual speed is off. The only was I can get a accurate spindle speed is if I put in max speed is 650. Then when I type in a value of say 500 in the Manual screen I actually get 500 on my hand held tach. The Velocity in the Motor tuning page is set for 675.

If I put any other number in the Spindle Pulley configuration screen I get the wrong real numbers on the tach. WHY?

I do not understand this at all and that is why I queried which screen you were talking about. As far as I can remember I have not set this up and have just kept the default which I think is 5000 for pulley 1.

Now how do I go about getting a faster spindle speed? Without changing my breakout boards etc. I spent allot of time and money setting all those up in my cabinet. I need increased speed without loss of resolution in the C axis Indexing.

Only option is to go lower count encoder or higher kernel. If my previous assumption regarding the true kernel speed is correct then increasing the kernel is unlikely to be an option. Lowwering the encoder count will hit on the resolution so the only other option I can see is to get a SmoothStepper which will allow you to get plenty of speed as it can pulse up to 4MHz.

Hood