MacOS – Mechanical Keyboard stopped working after upgrading to El Capitan

Without knowing what programs you have installed that could be doing that: Like some keyboard remapper...

• Log in as different user to make sure there is not something in you profile preferences

or

• Start in Safe mode to exclude other applications.

Then start applications one by one to find out who is doing it.

Also check this setting in System preference keyboard:

The fact that your computer shuts down at 50% remaining charge and also that your MagSafe LED remains orange makes me think that either the replacement battery isn't an official Apple part, that it is defective/DOA, or that your logic boards SMC is corrupted and needs to be reset.

If the battery is indeed new and Apple original than proceed with an SMC reset:

http://support.apple.com/kb/ht3964

This will tell the SMC chip to reset all power states and reboot so that it forgets the battery and MagSafe adapter momentarily and then rediscovers them.

Hope that helps