When I put mine in, I had to go to Step 20 in the B&M instructions too. You have to to remove the old tower before putting in the new one.
As I'd had no problems with the shifter before, when the new tower was in, I left the alignment tool on and ignored the marks I'd made and just let the cable ends drop in where they fell.
I didn't pull/stretch them like you did to get it to the marks. That may be causing some of your issues.
Anyhow, all good with my installation, no real difficulties in shifting, although I think I'm due for a front motor mount replacement.
BTW, it's 997, not 977.
Good luck!
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