Before you replace any parts, you should do a complete head alignment in service mode. Your print heads are seriuosly out of alignment. This will include bias - which insures the heads are straight and parallel to each other, then the vertical - which lines all the heads up with each other. Think of a squad of soldiers getting all squared up. These are both mechanical alignments, and you should go back and forth between the 2 until you don't need to make any adjustments. After these are done, you do the horizontal - which sets the head firing timing so all the heads fire at the same reference point as the first head. This is only done once. After this, you will do the bidirectional alignment, which insures the heads fire in the correct spot on both outward and return head movement, also only once. After these are done, you also need to do the user bidirectional alignment in regular mode.
The encoder strip can cause fuzzy printing and also shifting of the print between passes, creating a look similar to JPEG jaggies. It will not cause the color misregistration that I am seeing in your pics.
Do you have the service manual for this printer? All the alignments are clearly explained in the manual. It isn't a very difficult process.
Your heavy black issue sounds like a profile issue. You might want to try some other profiles and see if you get different results with the black coverage.
Let me know need some more guidance.
Jim Hancock