Quick reply.
(1) Congrats, and welcome.
(2) There is a technique of creating scaled alternate tuning tables (F Major, C minor, e.g.) that I have been told will create in effect a force-to-scale for arps. While there are only 12 user slots, it might be able to use embedded sysex to change tuning tables more or less on the fly. If I am right, you might be able to designate tuning table as a force-to-scale table and then uses embedded sysex to change the scale at the start of a song. Not sure if it would cause an audible glitch if you do it in the middle of a song. I think a tuning table is around 400 bytes or so.
That being said, IIRC you don't have to change an entire table. If I am right you can use on the fly parameter value edits and only change the notes that need to be changed.
I have addressed embedded sysex elsewhere.
(3) Re: editing arps on the fly - you can sort of do that with Prodatum--however, I believe each change causes a write cycle. So if you were to use a slider to move a step value through 32 values to get to the one you want, it is eating up 32 write cycles. I am not 100% sure on this, but I believe there has been some discussion of it.
I'd have to take a look, but I do remember playing around and changing skips and end-points on the fly. It might be possible to create an arp so you have skips in there that you can turn on and off. If it IS possible, it might come close to being to add a step (more like having it there, but deleting it). Again, I believe doing that a lot will eat write cycles.
(4) If you like softsynths, you might like the emulator x/proteus x. The arps have been replaced with function generators that are far more complex.
(5) You might want to consider getting an EMu Ultra sampler and slaving it to the Command Station. This will give you an unlimited array of sounds to choose from and still have the arps/sequencer. Hmmm. Now that I think of it, this might also help out with the force-to-scale issue. Not sure on this, though.
Hope this helps.
Steve