I am using an arduino pro mini 3.3v with the MS5541, and I think that the problem may be that the 3.3v version operates at 8MHz instead of 16MHz. I will try to put it on a scope and play with the timer values for the pwm, but I don't know if I will get anywhere. I havn't been able to find any tutorials about it anywhere.
I think that the other option will be to try to put a 3.3v reg on a 5v arduino and see how it works for me.
I got it so that I am getting the same calibration words repeatedly, but not every time, and I don't seem to be getting a response for D1 and D2 which are the digital temp and pressure readings. When I put a multimeter on it it looks like it is responding, so I am hoping it is a timing issue. I will try putting a scope on it and see what I get.