Hi Rob,
Regarding the maximum number of MST instances, I don't know any particular command for that. Usually, this limit is described in the Configuration Guide for the particular switch platform and IOS version. Have you had a look there? Let me know the switch type and IOS version and I'll gladly point you towards the proper document.
The MSTP and 802.1D or PVST/PVST+ cooperation is a complicated topic. I suggest reading these documents:
http://www.cisco.com/en/US/tech/tk389/tk621/technologies_white_paper09186a0080094cfc.shtml
http://blog.ine.com/2008/07/27/mstp-tutorial-part-i-inside-a-region/
http://blog.ine.com/2008/09/24/mstp-tutorial-part-ii-outside-a-region/
In a very short summary: if the outside world is pure 802.1D then only the MST instance 0 interacts with the outside world, and the state of the boundary port (Blocking/Discarding, Forwarding) influences all instances (and therefore, all VLANs).
If the outside world is PVST/RPVST then the boundary port replicates MST instance 0 BPDUs onto outgoing PVST/RPVST BPDUs on all known VLANs, and maps the incoming PVST/RPVST BPDUs onto the MST instance 0. There are some things that must be met in order for this "PVST Simulation" to work properly - see the referenced documents for more information.
Best regards,
Peter