I've been doing some research on the Y40. The good news is that your experience is not unusual (sort of good news, in a misery-loves-company sort of way). The bad news is that I don't believe your CPU downclock on battery is fixable, or not very anyway. I read a number of reviews (the one pasted below is representative) that indicate that your CPU/GPU/cooler/mobo combination throttles (slows down due to temperatures) relatively easily, is inconsistent in its recovery while plugged in, and won't self-recover when on batteries. This occurs even when the universal power settings are selected for performance, as I advised you to do above. This doesn't occur the same way, or even at all, with all Y40s, but with enough of them that there are plenty of postings about it online.
That being said, there are some steps you can take to help mitigate all this:
1. Keep your laptop clean, paying particular attention to keeping your fans and cooling vanes (at the exhaust vent at the lid hinge) dust free.
2. Make sure it's got plenty of clearance around the intake and exhaust vents when it's running.
3. Keep it plugged in as much as possible.
4. When it throttles, you can try rebooting to see if it can regain some performance. Apparently this works, at least temporarily, while plugged in - it may not do any good when on battery, but it's worth trying.
I'm also given to understand that the thermal paste used on the heatsinks leaves a little to be desired, both in quality and application. Depending on how comfortable you are with disassembling laptops, you might also consider pulling the backplate, uninstalling the fans and heatsinks, giving them all a thorough cleaning (canned air, q-tips, lint free cloth or coffee filters, and isopropyl alcohol (91% or better is preferred) and applying new thermal paste to the heatsinks. Costs about $12 for thermal paste and alcohol, takes maybe an hour if you've never done it before, and there are tons of tutorials and videos available online.
http://www.notebookcheck.net/Lenovo-Y40-59423035-Notebook-Review.124638.0.html