I revised the question to improve clarity of problem description and add additional details regarding steps taken so far. Early comments may have been posted before I revised question.
The problem is…
My furnace is short-cycling.
The furnace receives the call for heat, the inducer motor turns on, burners light, it runs for a minute, blower turns on, runs for a bit then flames go out, blower runs until the cool down cycle is complete, then it immediately goes right back into the start cycle and does it all again (lights, runs for bit, shuts off, lights, runs for a bit, shuts off).
This repeats indefinitely – it does not lockout or stop. I listened to it do it 5+ times in a row which is when I went down and checked it.
I am not getting any fault codes. I even sat and watched the whole process with the access cover off for over 10 minutes until I saw it turn off and there was/is no fault code (the lights never blinked at all). During operation the green, red, and yellow lights are steadily lit.
The furnace will only run for a few seconds to a minute when all the covers are on but when I take the top (burner/controls) or bottom (blower) access panels off, it will run for 15-20 minutes before shutting off. It does not shut off due to satisfying call, and I've even tested this by jumpering the red/white on thermostat.
My furnace is….
A Century/Heat Controller 92+ efficiency furnace, model number GUH92A072C5XE.
It's less than one year old (installed in january '16).
I did the install myself with the help of a friend who's very knowledgeable and has extensive experience with HE furnaces and installs. He's also been helping me try to remotely diagnose the problem, but we haven't figure it out yet.
The system is, I believe, sized appropriately for the house (manual J was done and also I got same recommended size from two different HVAC installers).
The duct work was existing from old fuel-oil forced induction furnace. Nothing was changed, just added a plenum adapter (cabinet width was same, height was different).
The furnace ran fine last winter and I never had a problem reaching/holding temperature.
I have old 1957 original (drafty) windows and doors.
Since last winter I've changed….
I added an A/C unit (split system – cased evap coil over the furnace cabinet, condenser outside) this summer.
I added a natural gas hot water tank (was still using the old fuel oil hwt last winter). The HWT is plumbed in before the furnace.
There were two large holes in the primary supply trunk (missing registers previous owner removed when they installed drop ceiling). They were dumping air above drop ceiling. I patched one of them, and I added a functioning register to the other. That was done this summer when I did the A/C.
Things I've tried so far….
- I checked thermostat was set to gas (not electric) and it was.
- I removed thermostat red/white and jumpered them on the controller to rule out thermostat issue. No change in behavior – it still shut off after about 15 minutes.
- I removed and cleaned the flame sensor. No change in behavior. Also flame light (yellow LED) is lit pretty steady when burners are on, so I don't suspect a flame sensor issue.
- The vent limit switch has some corrosion around the mounting bolts that I noticed – thinking it could be bad, I pulled the wires and put a jumper wire between them. I let the furnace run for a few minutes, and put the cover back on – the flames went out within a few seconds of putting cover back on, so didn't change the behavior.
- I started it up again with same vent limit jumper in place and actually pulled the jumper out while it was operating (simulating a tripped switch) and the furnace immediately threw the fault code. This makes me think it's not that switch that's the problem, or I'd probably be seeing a fault code.
- I took the inducer fan off – checked for water (it was dry) and checked for function (applied power with it removed and observed it running).
- I pulled the vacuum lines from the pressure switches and blew in them/sucked on them. The switches seem to work.
- I changed filters. The filters were very clean when removed – still looked like new even (I just changed them about 2-3 months ago) but I changed them anyways. These are the cheap fibrous kind of filter (not restrictive at all).
- When the blower comes on and furnace is running with all the access panes in place (normal operation) I can actually see the cabinet walls suck in visibly. This suggest there is a lot of negative pressure inside the cabinet. Thinking this could be a return air issue, I tried running without filters (no change in behavior) and I even removed the blower cover and opened the garage to house door (so as not to create positive pressure in house) and ran the thing (essentially giving it a GIGANTIC cold air return. The behavior did not change at all – still ran for roughly 15 minutes, shut-off, and started back up again.
Other things to maybe mention…:
So I'm not sure if any of these things are related or not, but I'm trying to give the WHOLE PICTURE here so I figured I would mention them.
- When the flames go out, they sometimes sputter/pulse before they go out. I can hear it and see the cabinet kind of pulse in/out when this happens when the cover is on. This doesn't happen every time, usually it just shuts off abruptly without any fan-fare. I'd say this happened maybe 3 out of the 15 or so times I sat and watched the furnace run until it went out today.
- It has done this same stuttering thing on rare occasion at start-up. It did this once out of the 15-20 or so times I started it today. When this happened, I could hear a switch clicking constantly during the whole startup procedure. I was fortunate enough to capture this on video! https://youtu.be/8jUNeCCnMgM
- Two days ago I came home to no heat – I had a pressure switch open fault. I pulled the vacuum lines from both pressure switches, blew threw them/cleaned out the hole in the plug they connect to, and started furnace back up. Fired right up and haven't got that code again. Not sure if this could be related.
MISC
Here's a picture of the furnace with the door off, in case that helps anyone understand what I'm working with.
Here's a picture of the vent piping coming out of the cabinet. It goes up, there are two 90's to help it get behind the main supply line, then a single 90 above the main supply, then its a straight shot out the wall. BUT! it reduces down to 2" to pass through the wall, and then there are two 90's on the exterior – standard "parascope" style. 
Best Answer
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.