Software synths for microtuning and score production - my know how for what it's worth;-)

Of the systems that I am familiar with you should be able to do what you want with:

Possibly limited microtuned audio with Sibelius; certainly microtuning scoring with Sibelius

certainly both with:
Cubase Mac or PC
Logic Pro 7 (Mac-only)

Cameleon as a plug-in VST or AU (only audio)
Melodyne Mac or PC (only audio)

.
If cost is no object, your best bet is Logic Pro 7 for audio and Sibelius for scoring.
To get the very best score images, you'll need to export the midi files to Sibelius, as the Logic scoring is pretty lame (but usable) in comparison to Sibelius.

Beware both Logic and Sibelius have very steep learning curves.

If you can tolerate pitchbend microtuning almost any system will recognise and play pitchbend, but only one note per midi channel can be bent at a time.

Also the guys at ZynAddSubFX that I spoke with last week at the London Sounds Expo claim that they can microtune their Linux system and use scala format tables.
There is also a scoring system for Linux, which I believe is called Soundgarten or similar. Check on Freshmeat for Linux systems

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