Like Andy, I now use ISIS for processing my spectra including calibration and producing spectral profiles to send to the ARAS database. It does have a fairly steep learning curve but the effort is repaid many times when you discover the range of functions for working with spectra which Christian Buil has built into it. There are lots of “how to” pages on Christian’s website about use of ISIS although I have never found a simple index to where they all are. It’s a bit of a treasure hunt to find everything but he has written up most of its functionality somewhere. The originals are in French but quite a lot has been translated by either Christian or Robin Leadbeater and Google translate makes a passable job of the rest.
I still use VSPEC http://www.astrosurf.com/vdesnoux/ which is free and useful for quickly looking at and comparing spectra and for most of the basic processing functions. I do find it a bit prone to crashing but I used it a lot in my early days.
I have used Astroart http://www.msb-astroart.com/ for many years for controlling my cameras and this also has a very good slit guiding facility which will happily keep the target in the slit for long exposures.
I’ve just posted details on the Forum about the BAA scheme to help members acquire an Alpy spectroscope if you decide to go in that direction. All the Shelyak spectrographs will deliver good results, you really need to decide whether you are more interested in seeing the whole spectrum which you get with an Alpy or LISA (higher resolution but more expensive) or in studying specific lines at much higher resolution with the LHIRES.
Don’t worry about asking questions, that’s the way to find out!