Exact same thing happened to me. The 1-2 shift from hell.
Took three tunes to get that kink worked out.

Tell Allen to look at Kinjo1977's tune and go by that to get your kink out.
I had to have the throttle, tranny points changed, and even had the Electronic Front Pressure selenoid changed out in my tranny. But changing the selenoid was just something I did to make sure it wasn't that.

Peace,
Ron