A998 & TF-1 - Harsh 2-3 shift

I have not tuned that roller, but you are right, 208/214/107 is not big.
And it's a roller, so the advertised would normally be about 246/252/107
But it's a Whiplash, so who really knows what the seat to seat is on it, Hughes doesn't publish it.
No matter, it can't be ridiculous.
But your idle is, and therein lies your problem. You need to get the idle down to a more sane 750 in Neutral, or less.Once your idle speed is down, the harshness will go away.
If you have to jam on the brakes when in gear, then the idle is too high or the stall is too low,or both.
If you cannot get the idle down,and the engine not stall when putting it into gear;something is wrong. The problem could be; in the carb,or in the compression,in the cam install,or the TC. It's usually a carb adjustment,but not always.
You need to;
Make sure the PCV is installed,correctly plumbed, and working
Set your T-port sync,Then set your idle speed with;timing and/or idle air bypass.
The other option is to install a TC with a higher stall.

That cam sounds great, when the tick-over is 650 in gear!