Congratulations on getting it running. The M45 might be too small for a 2.8L enging but it will be fun to play with.
I installed an Eaton supercharger froman SLK (M45) in my 2.3-16 and spent about two years sorting out the issues that you describe. My supercharger runs about 6psi and it is also noisy.
From your description, you have a vacuum controled by-pass valve. You will also need a pressure bypass valve (blow-off) valve to control transient pressures. When you rev the engine and close the throttle, pressure spikes of 30-40 psi will blow hoses.
If you do not have a wide-band furel air gauge, you need to get one. Running boost requires more fuel than the stock injectors can provide. I ended up with a complete digital engine management system. Here is some old info on my project:
http://members.cox.net/bettyv/16v/jim_16v.htm