I would suggest using the normal set up for scenarios (six survivors) as most missions were designed for six survivors. I divide them in to two groups of three so that one group must all take their actions before the other (same as a two player game). This way you can play any of the missions without the big disadvantage of being down two survivors.
Not a mission suggestion, but thought I'd share how I play solo - It helps me judge the difficulty of missions on the same level as when I'm playing with others too.
I mostly play two player but we do something similar with regards to fixing the order but take it even further. We fix the survivor order before we start by writing the names down in a list then moving the first player token down the list. This stimulates what would happen in a six player game and could easily be done for solo as well. I find when you get to choose activation order (even with the two groups of three suggestion) it's easier so prefer to add in the extra layer of difficulty.