The stock aluminum shift forks are weak (to say the least), and your new short thro shifter with the positive stops will help minumize the stress put on your forks by over shifting with your stock shifter.
I find it interesting that the PRO-5.0 people created this need for positive stops on their shifters to "protect" the forks and prevent over-shifting to sell more shifters and everyone believes it to the point it is all over the internet and on every forum everywhere!
If one tears down a T-5, T-45, or a TR3650 they will find a positive stop already in the transmission... The shift rail can only travel so far!
Mis-adjusted aftermarket stops have damaged a lot of transmissions by not allowing them to fully engage the gears.
Now, aftermarket shifters are great! They have a much better feel and they help you to not miss that 2-3 shift at the strip!
So, DO get an aftermarket shifter, but my recommendation is to throw the stop bolts away! They do nothing but cause trouble!