Missing 3rd on 904 trans

Background: Did a 5.9 magnum/ 904 trans swap on my 66 valiant. Both were used and the trans never had 3rd gear. I ended up doing a garage rebuild on the transmission and the 3rd/reverse clutches were definitely toast(pic of one of the clutches included). While I had everything out I installed a B&M Z gate shifter. I'm still missing a gear. Reverse works fine but from a stop manually shifting from 1-2 does nothing and 2-D shifts to second. I thought I had the linkage off by a gear but shifting to neutral and it goes to neutral. The car has 3.55 gears in it and I was running about 4000 rpm doing 65-70 on the freeway on the way to work(same rpm's it would turn at that speed before the rebuild).

Any ideas on what to check out adjust would be greatly appreciated.

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