My transmission isn't shifting smooth.

When my Dakota truck had this problem a friend suggested that the transmission filter might be clogged. I dropped the pan and cleaned it all out, and it ran like a top thereafter. You might try that first before more expensive efforts.

maybe go under your car and check if your shift linkage is somehow wiggled loose on your shifter or tranny. might help

It may be ATF filter inside or friction discs. I can't say it surely for Civic, but for CR-V 1995-2002 it is neccessary to disassembly AT to change filter. So, filter is being changed usually during AT total repairing.