First to clarify I'd like to run the H9000 with the 8/8 analog I/O , 16/16 usb and the 8/8 I/O Thru ADAT.  I believe i can use and process all these channels simutaniously  right??

Yes, you can use those audio I/O simultaneously.

Now i also know there are a max of 4 FX chains and you can use up to 4 algorithms in each chain.  What i'd like to know is there a limit to how many inputs or outputs you can assign to the chains , physical and software I/O?  

Currently, you can assign a maximum of 8 inputs to an FX Chain.  You can mutliplex the outputs to up to 32 channels.

We're currently working on increasing the maximum inputs to an FX Chain to 32 channels. That feature should be in the next major release.