The fact that you have to use a crossover cable is strange. The ATLAS E1 port should be E1 and not DSX, so it should be the same interface as the Alcatel PBX.
Have you tried another port on the ATLAS? It's possible it could be a bad port. You can also look at the ISDN L2 FORMATTED messages to see if the ATLAS is receiving any messages from the PSTN.
Since ports 2 and 3 work to user equipment, you can try using the crossover cable and connect either port 2 or port 3 (which should be configured as USER TERM in the ATLAS) to port 1 (which is configured as NETWORK TERM) and verify the D-channel comes up. If it does, then it may simply be the ATLAS is configured in the wrong roll, and it should be USER TERM to the PSTN (but this would be a very unusual configuration).
The configuration you have for the E-1 looks fine, with the exception being the "Outgoing Number Conv." may need to be changed to "As Dialed" and then remove all the NUMBER TYPE TEMPLATES (under DIAL PLAN and GLOBAL PARAM) so all number types are presented as UNKNOWN. If you look under the MODULE configuration you need to make sure the "TS16 MF" setting is set to "Disabled" - but that is the default setting.
Hope this helps,
had everything working call to the pstn p1 from slice p3 and m3k p2. did a last test of power loss, and d channels on p1 and p2 didn't recover. p3 is ok