Madoka parts a bunch of clouds with her attack and sends down a rain of light. Height of the clouds as nimbostratus, which are 6500 to 10,000 feet thick (an average of 8250 feet, or 2514.6m) and float at least 2000m off the ground (going with this average as they seem dark, but not enough to really be storm clouds).
= 2*atan(2880/(1617/tan(70/2)))
= 1.40188411 rad
= 80.32204286965289 degrees
Putting that through the angscaler gets 4244.1m as our diameter, and thus a radius of 2122.05m. Volume as a cylinder.
V = πr^2h
= π X 2122.05m^2 X 2514.6m
= 3.55737795e10m^3
Density of air is 1.003m^3.
M = 3.55737795e10 X 1.003
= 3.56805008e10kg
Next for our timeframe.
T = 1s/24
= 41.6666667ms X 23
= 2122.05m/0.958333334s
= 2214.31304/s
Now let's get the energy.
KE = (0.5) X 3.56805008e10 X 2214.31304^2
= 8.74739989e16 joules
= 20.90678750000000008 megatons
The second method is scaling directly to the cloud itself. Once again using the average thickness of a nimbostratus cloud (2514.6m).
79 pixels = 2514.6m
1 pixel = 2514.6m/79 = 31.8303797m
31.8303797m X 2880 = 91671.4935m
91671.4935m/2 = 45835.7467m
Once again calculating the volume as a cylinder, with the weight of air being 1.003kg per m^3.
V = πr^2h
= π X 45835.7467^2 X 2514.6
= 1.65969164e13
M = 1.65969164e13 X 1.003
= 1.66467071e13kg
Timeframe is the same as per above (0.958333334 seconds).
T = 45835.7467m/0.958333334s
= 47828.6052m/s
KE = (0.5)mv^2
= (0.5) X 1.66467071e13 X 47828.6052^2
= 1.90402995e22 joules
= 4.550740798279158561 teratons
And on a final note? What about the speed of Madoka's arrow itself?
T = 41.6666667ms X 10
= 0.416666667s + 2s
= 2.41666667s
Once again using the above average of 2514.6m...
T = 2514.6m/2.41666667s
= 1040.52414/340.29
= Mach 3.05775703
Final Results
Madoka parts clouds (low end) = 20.907 megatons
Madoka parts clouds (high end) = 4.551 teratons
Madoka's arrow = Mach 3.058