Compression test.

[renobruce]

Anyway, compression test with valves adjusted, cold engine and no frieken rage stuffed in the intake is 130, 120, 126, 126.

Now try it with the engine warm. They will go up even more.

[49er]

Your story has a familiar ring to it. I managed to forget to remove a small piece of rag from an inlet port on a race motor a few years back. The thing started roughly, then cleared and roared into life. Didn't realise what had happened until I found that I had only removed three rags. Cleaver stuff.
I'm not sure if your air box is similar to the 850's. If so, the reason that your figures didn't rise when you removed the rag from the airbox intake is probably due to the fact that some air is drawn in directly through holes in the bottom of the airbox. At cranking speed, the airflow would be low enough to enable sufficient unrestricted air through to the cylinders. You may even have an unsealed end cap on the box.
Checking cylinder pressures when the engine was hot increased my readings by 10psi from the cold readings.
At the end of the day, the cold pressures are what influence how well you can restart an engine that has sat for more that 3 days, especially in the winter. Engines that have sat for days are usually hard to start with the throttle fully open. One exception is when they have been flooded.