Agreeing that you have expertise in hardware swapping and also assuming software expertise, reinstall all the parts and perform the clean install of the MacBook using a USB keyboard and mouse and perform clean OS X install as it might suffered kernel panic or kernel extension problem. Before reinstalling clean the connectors of the trackpad and keyboard in the logic board with ipa. All the best
Yeah the outer screen will have that circle when the inner screw pierce through the screen from the inside. I agree with ben. Long screw has been used instead of the original screw to hold down the home button.
Have you removed the battery before replacing the LCD. If not, remove the battery first and with display connected and press the power to remove any static charge in the components. It could give a chance. Careful while removing.. Don’t use too sharp objects as spudger and double check the battery connector while replacing.