I used to create a set of Pipe Organs on Roland XP-80, and although it is a completely different machine, I might give you a couple of tips.
First, XP-80 has had terrible Pipe Organs and only one Pipe Organ waveform. Pipe Organ sounds, three of them, mostly faded out if you hold them long enough. They didn't sound natural. But, it's sound was based on 4 wave elements and I used mostly these waveforms, combination of 2, 3 or 4 elements, to create convincing Pipe Organs:
Pipe Organ waveform for basic sound, heavily manipulated by filters, specially LPF
Flute (non vibrato) for distinctive pipe-ish sound (Positive), also a bit closed by LPF mostly (try other filters though)
Clarinet for basses (pedals) and even for main sound (If you keep it for basses only, than it should fade out as you play toward the right end of the keyboard)
Sine wave for the Principal emulation
Some none vibrated mild
Electric Organ waves (similar to sine) for added character - but I pushed them in the back of the mix.
Make sure you remove any "click" on attack, which is usually found on Electric Organ waveforms, and even Clarinet. It should have a mellow attack. Put "attack" value a bit lower.
Since AFAIK Microstation does not have that 4-element structure of the sound, you can still use Multi section to develop each of the above sound from above and mix them together. So what you do is, you develop each element of the Pipe Organ sound, based on the above waveforms, and make individual presets out of them. In the Multi section, you put them together and manipulate the volume of each part.
Remember, you have to see which one of the sound should dominate, and which one is to be pushed in the background, as you create the mix. The main work while preparing the programs is to play with Filters, Resonance and Cutoff.
Also, remember, you have several Pipe Organ waveforms in Microstation, and try first doing something with them, by playing with Filters, Resonance and Cutoff as they change the character of the sound most directly and drastically. The Pipe Organ waveforms are Multispamples from 0042-0047. So you have six of them.
Just be patient in your work. I am sure you will be surprised how good your keyboard may sound.
Good luck!
