If your just cruising, it's fine, but if your racing it, you go from max line pressure on manual 2nd to standard line pressure in 3rd, the computer doesn't automatically know that's what you did, it has a delay while figuring out what gear to go in that causes a bigger than normal Rev up durring the shift. Then as it is engaging, this causes a shock load on the trans (like when the tires suddenly grab after a burnout) . You may be fine with the upgraded hard parts, but just something to be aware of.
I've also heard stories of it going back into 2nd and bouncing off the limiter before shifting to 3rd, so it may be a slow run, and make sure to your limiter is set properly.