Basically yes, you are on the right track. Your eye separation (IPD) needs to affect your modelview matrix (post head modelview translation) and your projection matrix (defines relationship of each eye to individual displays in the HMD, taking optics into consideration).
The other thing you need is a head tracking device which also affects your modelview matrix. HMDs tend to sell separately from the devices used to track them (magnetic and optical).
I don’t have any current info on cheap HMDs, google it, I think there are even some consumer products out now.