Advice on wiring connector

[WhatdoIdo]

Can anybody tell me how to reattach this connector (and what it is), see pics. I had to unplug this for room to install a Mountune Quick Shift part (needed room to get the ratchet under the shift bar). I came out just fine, but now trying to reconnect it it seems the pins do not want to insert into the plug.

 

[Intuit]

Seal is probably out of place. Ran into a similar issue with one of the headlamp plugs.
Use your cell phone cam to peak into places your peepers can't reach.
Might experiment with trying to reach from underneath.
Pull the plug and get a better look inside the plug and jack on the other end.
Make sure the seal is properly seated and the male pins aren't bent.