I have a suggestion for for the chip boost as well.
Why not have an auto chip boost. Then you can introduce a new upgrade for auto chip boost.
What auto chip boost would do would automatically do chip boost for you for each kill for the selected gem. The down side to to counteract this a bit should be that auto gem boost uses more than 1 gem but for the same effect as 1 gem. Then the upgrade for auto boost would lower the amount of gems it uses.
Just replying to your message about the gem system. What if you made it cost 100 gems each to fuse for the next level. Decrease a lot of the earlier gem amounts, and make it so you dont end up with the higher gems until + levels. You don't even need to allow players to hit the top gem in their first rebirth. As pointed out by KidA1515 Once you get the top gem there is no point in using lower gems anymore, which leaves you with thousands of lower level gems. The progression seems to fast.