I'd cast a long look at that SSD, and I'd run memtest all night on the memory too (which I noticed you didn't sell...).
Highly recommend you do this, even though you bought a new mobo and CPU.
Will I notice any drop in performance going to a mini-itx PC?
If all the components are the same (besides a smaller mobo) then performance would inherently be unchanged. Mobos don't do anything significant for the performance of a PC at stock or near-stock speeds. The only noteworthy differences between just about every motherboard on the market are: size (# of expansion slots), OC-friendly / higher quality components, and added features (eSATA, PLX chip, # SATA ports, built-in WiFi, etc). The size of a motherboard alone doesn't affect the performance of the system. Having a smaller mobo will only really limit how many expansion cards you can strap onto it (aka. 1 with mITX).
Last time I used one I remember being upset with its power.
The system you're referring to probably had low-power components (like Egg
said) to either 1) keep heat in check for a case that had poor ventilation, or 2) reduce system cost. If it didn't have an SSD, that would obviously adversely affect your opinion of responsiveness since you're used to running on an SSD in your "main" system.
Main: i5-3570K, ASRock Z77 Pro4-M, MSI RX480 8G, 500GB Crucial BX100, 2 TB Samsung EcoGreen F4, 16GB 1600MHz G.Skill @1.25V, EVGA 550-G2, Silverstone PS07B
HTPC: A8-5600K, MSI FM2-A75IA-E53, 4TB Seagate SSHD, 8GB 1866MHz G.Skill, Crosley D-25 Case Mod