I'm pretty sure this topic has been discussed many times over, but this may be a little different. I bought my 03 GT last year and loved it right away. I upgraded the suspension and a few other things but the transmisson would occasionally grind when going to 2nd. I thought it was me but after a few months with the car I realized it was the transmisson.

I did some research and read about changing fluids and filling with only 3l instead of going to max fill. After this it was a bit better but I was still getting a notchy feeling into 2nd. I paid a visit to Dasilva and he suggested pro 5.0 shifter which was a blessing. I removed the steeda shifter (installed by the previous owner which BTW was meant for T56 not my T3650) it was a huge improvement.

But I find the shifter or rather shifting from gear to gear pretty stiff, any gear. It's not a smooth experience. I'm a new mustang owner but I have driven others. I find I have to put too much effort into shifting. I hope this makes sense.

 

Could it be the pro 5.0 shifter causing it to feel stiff?

 

I've never had a pro 5.0 but I had a few b&m shifters and they were quite notchy but I preferred that over the stock shifter. First thing to try might be to look for a stock shifter. You can probably find one for free and try that. If it doesn't improve you may have other issues.

 

There was a tsb on this issue, and Ford would fix the issue if the customer was not happy, and pleased on how the 3650 shifted. I had mine repaired/built, and it's still catchs second slightly, and my GT has 65000 k's to date. I think it's just the nature of the 3650.
How bad is it for you? How many k's?