I have two unrelated thoughts here.
1) Those holes you are talking about toward the back of the stove - they aren't there to supply secondary air! Quite the opposite actually, in fact if they were supplying secondary air they wouldn't be getting clogged up. Combustion air for the primary firebox actually comes from the front/top of the stove. Those holes at the back are there to deliver gasified wood to the secondary combustion chambers. If you add your own shields over them, they won't do what they were intended to do. That said, plugging some of those holes might actually improve performance, who knows? It could force a more concentrated, and hotter supply of gasified wood though the main opening (i.e. the throat).
2) To illustrate a point about emissions vs. a stove owners perceptions, look at the Omni study if you have some time. Do a search on "defiant" to pull out everything on the person with the Vermont Castings Defiant Encore Catalytic stove (EPA Phase II certified to burn at 1.6 g/hr).
Actual quotes from the study: "The Vermont Castings Defiant Encore (Appendix A, Photograph 31) is in good working
condition, including the door gaskets and refractory elements."
"The owners indicated that they are happy with the stove."
During the first of two full week study periods with this stove, it was burning 98% of the time. By most measures, it SEEMED to be burning great, in fact this person used nearly half the wood that some of the other stoves burning full time consumed. The average indoor temp was a cozy 71 degrees F. And yet the emission rate was a horrible 23 g/hr! (remember its certification value is 1.6 g/hr)
So the owner is happy, their house is warm, they aren't using that much wood, and yet they are polluting like crazy and not getting anywhere near the EPA certification number on emissions. So just because someone says they are happy with their stove, or they are heating their house fine, that doesn't necessarily mean they are burning clean. And for what its worth, the average non-cat EPA phase II stove burns cleaner over time and under real world conditions than the average cat stove in multiple studies that I've seen so far. But perhaps these everburn stoves will change all that