Yea I talked to a good friend of mine who is high up at Dodson Motorsports, which makes high performance transmissions for the GTR, Lambo's, you name it. He told me, its just that transmission. They will all feel a bit different and I just need to get used to the feel of it. I asked about a Pedal Commander and he told me it will end up messing up the way the transmission shifts in other gears too. So by fixing the problem with 1st gear, I may have problems later on with others. So yea, I think you are right and I just need to get use to the way the throttle feels, especially with the new 9 speed transmission.Give yourself some time to get used to it. What you described does not sound normal.
Every Titan since the beginning of time (2004) has drive-by-wire throttle. I was skeptical at first, but mine (2004) has been flawless for 17 years. People who borrow it (i.e, my brother who has Chevy and Ford) say "your throttle feels weird". It doesn't feel weird to me.
Also, my transmission (5 speed) was the smoothest shifting I've ever experienced in any vehicle. Couldn't even hear or feel most shifts unless you had one eye on the tach. Again, 17 years later, it's still good. When rounding a corner in my suburban neighborhood at <20 mph I sometimes feel a small lurch as it's downshifting or upshifting, like it's momentarily confused (for 0.5 seconds) as to what my intentions are, but it's very, very minor.
Got my first scratch on the top of the tailgate (plastic part) last night, moving furniture so I had a small sad moment, but I officially have a truck now lol. Look forward to writing stuff in forums 17 years from now with the same truck Thanks for the insight.