You will lose percentage if you get less than 500, just pass 500 and go to Beclem (You can do 650 if you want to).
You won't lose any point if you didn't calliberate all the towers (in fact, you don't need to), but if you successfully callibrate all the towers, you'll get good goodies in Chapter 5 as well as a GG.
You will lose point if you don't beat Shinra in Luca, you will also miss Lady Luck (You can still get Lady Luck in Chapter 5 but Shinra is more tougher) and a GG. Echo Combo/Break is your only choice to win.