The cable might be a little too tight. I'd drive it first to know for sure, but it makes sense to me that if the throttle is tighter, and it's shifting too soon, then the operating pressure controlled by the cable might be a little too high (this is all based on my research - I don't have any practical application). Now that the TV cable is [essentially] attached to the throttle linkage, there should be a little bit of difference, but not hugely noticeable.
Also, check the routing of the TV cable to ensure the cable is not pinched or have a too tight radius anywhere - which would cause cable binding and make things 'stiffer' to operate. You want a little bit of pressure on the TV cable to keep the operating pressure in the right range... but the cable shouldn't require much effort to operate at all.
Also, don't drive it too much until you get things properly set-up. Having no (or too low) pressure on the TV cable will cause the transmission to burn-up... and having too much will likely cause similar issues that might just take longer to realize.
Glad to hear you got it all back in and working. Now you just gotta fine-tune everything and enjoy!
BTW - how's do the gear ratios feel (should be essentially the same as the FMX, until OD - might feel a slight difference because of the 4R70Ws... but probably not as much as you think)? Did you get the rear gear swapped out yet, or was that going to be a later project?
