I just changed my tranny(96 civic) and the cover came off without taking off oil pan, but if I remember correctly on my 89 accord I had to take off oil pan first, if I remember correctly. It is a cover the protects debris from getting into your clutch/flywheel area. I would not run without it and if you have time get another one that is not fuxored up.
Here is a 88-91 CRX manual it may tell you the order to taking that part on and off.
I did not see a reference to taking that part on or off to get tranny off.