Before worrying about cleaning up your digitized audio, have you investigated cleaning up the vinyl? It's a LOT easier to get rid of the pops and scratchy sound through getting the crud, dust and junk off the disc BEFORE you import it.
I've digitized a number of old LPs (and 45s!) and the very first thing to do is to clean that puppy, but good! I have used a fine brush followed by sponging with high-percentage rubbing alcohol, and sometimes a rinse with alcohol. The grooves tend to collect dust and junk from the air (especially if the disc lived with a smoker), and alcohol dissolves most of that pretty well. Of course you let the disc dry afterward, but that's one of the reasons to use the highest concentration alcohol you can get-it dries much more quickly. I can get 91% isopropyl at the drug store all the time, so that's what I use.