We are using a X9QR7-TF+, is it possible to just use CPU1 and CPU4 slots equipped with let’s say E5-4650? Is this motherboard fully functional (except the onboard LSI 2208, which is powered by CPU2) is working with just these CPUs?
Yes it is. Just keep in mind that if you want to upgrade to 4 CPU's later on, they need to be of the same stepping.