Gas Furnace Filter

QUESTION:

I had a new 90% efficiency Heil forced air gas furnace installed this past summer. I find that, even when the house thermostat is below the target temperature, the furnace turns off after some time (10-30 minutes), stays off for some minutes, and then turns back on. This goes on until the temperature reaches the target value. Its effects are particularly noticeable with the cold weather we've been having in the Northeast as it takes the house a long time to heat up.
I've done some google searches, and the best theory I've found is that the combustion chamber is overheating and that a temperature limit switch kicks in. This may be because the overheat is real, or because there's a faulty switch. If the overheat is real, it could be caused by insufficient airflow, possibly caused by a dirty air filter.
One time, the burner turned off while I was watching through view port. It attempted to relight three times and then it stopped. I them recycled the main switch and it once again tried to relight without success. Repeated several times in quick succession, with same result. Then, I waited several minutes, and recycled again. This time the burner lit, but the furnace stayed on for only several minutes. This really seems to validate the sensed overheat condition.
I've checked the air filter, and it seems OK. Can I run the furnace for a while without any filter to see if the condition improves? I assume that a filter, even when clean, will restrict airflow.
Any other theories or suggestions? Maybe this is normal for this type of furnace? The installer has been to the house twice and hasn't really fixed this.
On a slightly different topic, I have a question about thermostat management. My wife and I both work and we like cool temperature for sleeping. We program the thermostat to 60 deg F at 10:30 at night and to 72 deg F @ 2:00 pm so the house is warm when we get home at 5:30. Our house is not that tight. BTW, we live in Worcester, MA. Is this too wide a swing? Can anyone point me to a site that explains how to manage the temperature to achieve optimum efficiency?

ANSWER:

See pictures at http://www.pbase.com/raduray/furnace .
The supply duct on top of the furnace is 20x20 The return duct on the side of the furnace (where the filter is) is 18x22 The filter is a fiberglass mesh type, about 3/4" thick, no frame, and is clean. There are 15 supply registers. Three of them are turned off. The ones upstairs have very weak flow, but that problem existed with the old furnace as well and is another problem.
While I was taking pictures, the flame went out. It tried to restart three times. The first two times, the ignition glowed, the pilot came on and the main burers failed to start. The third time, the ignition glowed but the pilot failed to come on. The light on the valve flashed the heartbeat (I found the flash rate description in the install manual). I tried to recycle the main switch, but no joy. Went upstairs to discover the temperature had reached the thermostat target. I do find it strange that it would try to restart (and fail) even though the shut-down was commanded by the thermostat.
I'll continue to monitor, and if I catch an unexpected shutdown will send the flash data on the valve lamp. Unfortunately, the weather has warmed up so I don't expect the furnace to have long 'on' cycles.


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