First of all, good luck to you! I can't speak to all of your questions so I'll take a stab at the ones that I have thoughts on.
1) Software - You owe it to yourself to also consider Hoochware as your distillery management solution. Great product, great service, highly recommended.
2) Marketing - We have been using Groupon and have been very satisfied with the results. Most of our tour customers are Groupon voucher holders. We are reaching people outside of our immediate area and most tell us they had not heard of us prior to seeing our deal on Groupon. Our Groupon deal is structured as discount on our tour which includes a cocktail and a tasting. We've found that most tour customers either stick around for another cocktail or take home a bottle or two and/or some merchandise. If you can break even on the tour (after Groupon takes their cut) you will generate a decent amount of revenue on those folks with their after tour purchases.
I guess t-shirts or engraved glencairn glasses are the most popular non-booze item but to be honest, the non-booze stuff doesn't really make that much of an impact (at least for us).
3) Hours - our tasting room is open from 11-7 on Thursdays, Fridays and Saturdays for tastings, bottle sales and cocktails. Since we're at the distillery on Monday, Tuesday and Wednesday we open the tasting room from 9-5 but only for bottle sales and tastings. Since we have a couple people there at all times, taking care of a customer doesn't really impact production on M-T-W since we can always keep one person back in the shop - having only your master distiller could present a problem if he/she is being pulled to the front too often.
4) I used a consultant to help me with my DSP application but I did the grunt work and was the only point of contact for the application. That way I had a sounding board for my answers but I was able to be very responsive to the TTB since they were reaching out to me with any issues.