first off, WELCOME to the forum!

next, the first pic shows your cowl drain. the crack is not important, as it's only for water that enters the cowl vents in front of the windshield.

the second pic shows mounting holes for an option your car didn't have, likely either abs, or an earlier blower resistor box mount, possibly even an euro option.

third, it's the vacuum for the egr controls. if the hoses are still connected on the other end, it could indeed lower your vacuum so the doors don't work.
all the cars have the 5 hole, only the upper left, and lower left two holes are open, just plug the two back into the lower left two holes.
you could also remove the hoses altotether, and plug the connections where they connect by the IP, and the EGR will no longer function. do this to test your door locks.
don't forget to reconnect the hoses, so the Soot heavy exhaust can get back into your intake and satisfy any emission inspections...

__________________
John HAUL AWAY, OR CRUSHED CARS!!! HELP ME keep the cars out of the crusher! A/C Thread
"as I ride with my a/c on... I have fond memories of sweaty oily saturdays and spewing R12 into the air. THANKS for all you do!

My drivers:
1987 190D 2.5Turbo
1987 560SL convertible
1987 190D 2.5-5SPEED!!!

1987 300TD
2005 Dodge Sprinter 2500 158"WB
1994GMC 2500 6.5Turbo truck... I had to put the ladder somewhere!