New System Slower than Old System

I recently built my first rig, one that should be pretty fast. However, things load slower than my 4 year old system with less impressive specs. Also, at times, something must occasionally be using a lot of cpu cycles since my keystrokes are not recognized for maybe 3-5 seconds and then the display catches up. I've looked at my running processes and can't find anything that stands out as odd. While I'm not a technical expert, I have enough experience with hardware, Windows and common apps that I rarely run into a problem I can't solve. I would like any suggestions anyone has to get to the bottom of my problem. By the way, these issues have been present since I first turned on the system and installed Windows and I'm extremely careful about downloading questionable apps from questionable sites.

Here are the major system specs.

Asus Z87-PRO ATX LGA1150 Motherboard
Intel Core i7-4771 3.5GHz Quad-Core Processor
G.SKILL Ripjaws X 16GB (2 x 8GB) 240-Pin DDR3 1600 (PC3 12800) / F3-12800CL10D-16GBXL
Samsung 840 EVO 250GB 2.5" SSD
Western Digital BLACK 1TB 3.5" 7200RPM / WD1003FZEX
Asus GeForce GTX 650 Ti 1GB / GTX650TI-O-1GD5
Windows 8.1 Pro

I'm running Avast Free and Malwarebytes. I don't using any off-the-wall or uncommon apps. I have used Black Viper guidelines to shut down unused services. My only enabled start-up files are as follows:

"C:\Program Files (x86)\Google\Chrome\Application\chrome.exe" --type=service
"C:\Program Files\AVAST Software\Avast\AvastUI.exe" /nogui
"C:\Program Files (x86)\EMET 4.1\EMET_agent.exe"
"C:\Program Files\Realtek\Audio\HDA\RAVBg64.exe" /DTSU2P
"C:\Program Files\Realtek\Audio\HDA\RtkNGUI64.exe" -s

Any suggestions? I'd like to be able to take a look at what's happening when, for example, my keystrokes are not recognized immediately, but not sure how to accomplish that. I've tried quickly looking at task manager, but the duration of the problem is too short.

Thanks in advance for any ideas.

Wired keyboard or wireless ?

Wireless keyboard & mouse.

Might have some communication problems between KB/Mouse and rest of the system, specially if it is WiFi type. I would first check with a wired KB and drivers for wireless ones.