The main library for dealing with spherical harmonic transforms that I've used is Healpix. But I'm not sure you need that (it's also not available in Mathematica: it supports C, C++, F90, IDL, and Java).
If you just want to do a simulation, you can do it easily by selecting a fiducial ##C_\ell## spectrum, and then select the ##a_{\ell m}## values from a normal distribution with a variance given by ##C_\ell##. Mathematica should make this job easy.
If you assume a circular beam, it has the primary effect of suppressing the angular power spectrum. I forget the exact formula (you'd have to hunt for it), but it will look something like ##\tilde C_\ell = C_\ell e^{-\theta_{FWHM}\ell}##. There's probably some factors of two or pi that are needed to make that work. Note that even though the angular power spectrum is suppressed, the noise is not suppressed by the beam.
You'd also have to convert the map sensitivity of ##1\mu K## into a noise level for the ##a_{\ell m}## values.
Finally, the sky coverage has two main impacts:
1. It introduces correlations between the errors. This isn't a trivial effect, but you may have to ignore it for simplicity.
2. It reduces the effective number of modes you can measure per ##\ell##. With a sky coverage of 40%, this means that for ##\ell = 2##, which has 5 modes, you'll only have 3 independent modes. This has the effect of increasing the standard deviation of each ##C_\ell## by a factor of ##1/\sqrt{0.4}##. This is a rough approximation, but it's probably what you'll have to do.