My concern is the network more than the router, I fear the great help you received was done in the knowledge it was a standalone system they were dealing with, I can't see anywhere at the start of the help that you had said you were on a network, and as such you were not instructed to remove the system from the network before starting the process of scanning etc, it was only at the end I noticed this mentioned (apologies if I missed an earlier mention).
I am no pro, but my limited understanding is that if in a network situation, the 1st thing is to isolate the system from the network, so there is no chance of the infection(s) passing over the network to the other system(s) and infecting them, which is my suspicion here, then checking the other systems for this possibility before connecting back to them again, so my gut says all the systems should be isolated and then scanned independently, and cleaned if necessary, but more importantly given the all clear before returning to the network, this should stop any cross contamination from happening, without this as soon as a clean computer is added to an infected network it becomes infected again.
My advice is raise this query with Ken, and see if he feels my concerns are valid or not, but as an FYI to ANYONE reading this (not just the OP), is when in a network make sure the person helping you is made aware of this before starting any work, their time is valuable, and they are very busy guy's and gal's, so giving them ALL info about the setup you have can make a big difference in how they approach it, which ultimately not only saves them time (having to do the job only once), but also saves you time, and frustration.
As to the router, I have never heard of an infection hitting such a device, but again I am no pro, and I guess anything is possible, should you want to try and see about this, my gut says upgrade (if available) the firmware, or if not available reflash the firmware it already has, it's the quickest surest way I can think of resetting it to it's factory state (from a clean system). and making sure there is nothing hiding in there to stop this happening, this is an extreme worst case thing that I don't think is happening (or even possible at this stage in infections), but if you want a belt and braces approach, this would be it IMO.
So have a quick word with Ken about this, and go from there is my best advice ATM.