Final final update (I hope). Putting the TOR and xover back on did regain some of the lost HP, but the bike didn't pull as strong before the jars. Final HP was 173 and the sorry tq was 138(!!!) quite high in the rpm range. Still strange the jars flowed better (ran lean) and made less power - I guess higher flowing pipes are not the answer, but I am done messing with it since there is no clear cut direction or promise that it will get better.
What a huge waste a money and time. A fool and their money eh? Apparently I would have bought magic beans with that cash anyway. Wish I would have just done triples and pipes.
Plus side - nothing is broken, bike runs well, is better leaving a stop than before (no more riding clutch a silly amount), a/f ratio is good.
I will say progressive 440HD shocks are amazing. That was money well spent.