My setup process:
1. Remove rear mech and align mech hanger (special tool to do this – highly recommended!)
2. Set high screw with gear cable slack – top jockey wheel should be perfectly aligned with chain and smallest cassette sprocket
3. Adjust cable so that all gears are indexing nicely and that, when in the correct mid gear, the top jockey wheel is, again, perfectly aligned with chain and cassette
4. In the largest rear gear, adjust the low screw so that it _just_ touches when jockey wheels are perfectly aligned. I then back it off a tiny bit to allow some small over-shifting here to let the shifter lock in soundly. This is a bit trial and error, but it’s quickly done. Don’t back off too much or you can lose the chain into the spokes and that can cost money…
5. Shift up and down the gears. Each gear should shift to the next largest cleanly and sharply without over-shifting (i.e. pressing the shifter past the shift point). Likewise, shifting larger to smaller should be sharp and without hesitation. If it’s not, revisit step 3.
(Note: I’ve not covered the B-screw adjustment, as this is typically only needed with a new mech and not with a re-cable.)
If after all this, it still doesn’t work, then replace the cables as modern setups are sensitive to cable friction. Also check for any play anywhere in the system and make sure all cable end ferules are securely located. Once you’re happy, readjust after a week or so, but don’t expect to fiddle with it much after this as, once setup, it should be pretty much maintenance free.