My process is very, very similar to yours (and I'm a programmer as well).
The one thing I never thought of is using graph paper. Seems like an obvious choice once you said it.
What I do instead, is print off a template that has the outer lines of the panels and the logo for the comic.
I also have a sheet that has my lines for dialog that I can put behind the template sheet. I pencil in everything on that template sheet since like you I don't plan to ink over the pencil.
From their we are very similar. Instead of a light box, I have a homemade light table. I had left-over lexan from a project and some composite hard board, so I just routed out an opening where I could pop in the lexan. I use architect's tape (remarkably like plain ole brown tape) to attach my pencil rough to some bristol board. I like having them attached so I can spin them around and hit different angles without worrying about registration.
I use some PITT artist pens to do my borders. I trace over the lines of the template onto the bristol. Lately I've been using those pens to do my lettering as well. Much faster than using the dip-pen. I still like the results better on the nib with India Ink.
Next I ink my scenes. I prefer to do it with a brush, but it takes great concentration not to screw that up. I tried doing a recent comic with the PITT brush pen and I hated how it turned out. The vast bulk of my Funzietown stuff was done entirely with the nib pen with solid black areas filled in with the brush. My favorite brush for filling large areas? A wide Crayola brush I cribbed from my kids supply of stuff they didn't use any more.
My main brush is a #4 Round that I picked up at Hobby Lobby (also the source of all my bristol, etc.). Although there are better art supply stores in Atlanta, none are close to me.
I come back in and do shading with a set of Staedtler technical pens.
From there it is a scan and clean up process.
I use GIMP occasionally, but my main tool is Paint.Net. It is just a bit easier to use for simple stuff.
I upload directly into my comic/blog software that I wrote using aps.Net MVC. It has a few niceties like holding a buffer and only showing stuff on its pub date, and suggesting the next pub date when you upload, etc. Still very much a work in progress, but I like it better than my last system which I wrote in asp.net webforms. To be fair, I stopped working on that version when I started learning MVC.
Once I decided that a) I have no readers and b) I will never make money at this, I began to experiment a lot more. Some have been successful, some dreadful (curse you PITT Brush pen, followed by coverting everything to pure black on the computer!!!), but since I have no one to complain, it doesn't matter. That is liberating.
The one thing I did significantly differently was my Gun Baby On The Moon Hunting Dinosaurs. I inked that completely on the computer using Microsoft Expression Design 3 and my mouse. NOT an optimal way to draw, but it's what I have. Design is Microsoft's attempt to make an Illustrator like program. No where near as good as Illustrator, but better than nothing. I think with a Wacom tablet I could get used to inking digitally, but I really do like ink and bristol. I enjoy that process. Since I'm not doing it for money and readers, I might as well do what I enjoy.