A998 & TF-1 - Harsh 2-3 shift

I shouldn't experience harsh engangement running 1000rpm at idle?

I can't recall removing the accumulator spring. If a blocker rods needs to be in place when removing the accumulator spring, then no. Doesn't the accumulator affect 1-2 shift as well (1-2 shift is perfect)?

I forgot to mention I run a Hughes Perfromance XTM torque converter, which is pretty tight.

A 1k idle very well could cause harsh engagements, and the blocker rod doesn't have to be there if the spring is not for the trans to work.
It should if the spring is removed, but that doesn't mean it is or was put in.
It's possible there is no spring and also not have the blocker rod. (which you also wouldn't want)