What is this built on? A slab? That does not look like a clamping drain designed for a shower to me (but I'm not a pro at this). If there's no liner, then you owe it to yourself to redo the entire pan since you've torn out the most of it anyways.
A rubbing stone can smooth off high spots, and you can use thinset or a medium bed mortar (often called granite and marble mortar) to fill in divots that are deeper than say 1/4" with the medium bed stuff. A thinset shouldn't normally be used deeper than about 1/4", but a medium bed mortar can go up to about 1" (depends on the brand).
If that drain isn't proper, or if there isn't a proper liner, OR, if that liner is flat on the subfloor, you should do the pan over. Many people, including some plumbers, seem to think that the tile is the required sloping waterproof surface...it is not. The LINER must be sloped to the drain, since slowly, some moisture will get underneath the tile. It needs a sloped path to migrate to the drain (and your drain not only seemingly missing the clamp for the liner, does not appear to have the required weep holes to allow any trapped moisture to make it to the drain).
For expert help on tiling, check out www.johnbridge.com.