Does this look like a crack in the heat exchanger

Fixed! Turned out, it was an issue with the condensate drain line. I had moved it and it had become just ever so slightly raised, so that the line had become double trapped. The collector was filling up with water, and tripping the secondary pressure switch.

The reason I wasn't getting a code, was because the water was gurgling, or bubbling, as the negative pressure pulled the water back up the condensate line. This caused the pressure switch to fluctuate rapidly, which is also what caused the sputtering flame problem. This rapid fluctuation, which was picked up by a multimeter, was too fast for the control board to actually register a fault.

Fixed the condensate line, and all is well.

Haven't been able to explain the cover on/cover off phenomenon, may have simply been coincidence. It ran all night, all buttoned up, without issue.

This question unfortunately can not be answered without a lot of data that is usually very difficult to obtain. First off there is no such thing as a time limit on filters. The same filter may last 1 month or 10 years depending on usage and the amount of airborne particles. If the new filter has more back pressure than the existing one then it has the same effect as a dirty filter, more back pressure. Too much back pressure and the heat pump will over heat. The bad part is most manufacturers do not publish their pressure ratings. The only way to tell is to take pressure readings with a magnahelic gauge and compare the reading to the published air flow for the air handler. As a general rule of thumb the thicker the filter the better the air flow and the base of most air handlers are too small to accept a proper size filter so I generally make the filter cabinet larger than the air handler opening. Sorry I can not give a more direct answer but there is no guarantee that the system was designed properly in the first place and the only thing that matters to your equipment is air flow. Give it enough airflow and the equipment will be happy regardless of what kind of filter. One final thought, people tend to over emphasize their filter. The filter is one small part of keeping dust down. The filter is only doing its job a couple hours a day unless the fan is set to continuous. Only a small percentage of particles actually finds its way to the filter anyway. I would argue that if you had 2 identical homes, one with a MERV 8 filter and 1 with a MERV 16 filter there would be no noticeable improvement in the air quality since most particles are not airborne long enough to make it to the filter. Any filter that fits snugly in the filter rack and provides at least the same air flow will be fine.