There are 2 ways to size a chain.....small/small or big/big. Depending on you setup either has the potential for causing issues. There is absolutely on reason why you should be taking out links. ZERO. NONE.

Chain shortness: Primarily determined by your small/small gearing. Since you 34/13 low/low hasnt changed you need to add back all of those links.
Chain length: It needs to be long enough to wrap the big/big gearing. You've added 8 teeth to the back which means you need to add about 4 links to your original chain length.

Have you ecked the derailleur hanger alignment? I know this is C&V but do yourself a favor and buy a full Shimano indexing system.