I think you might want to keep those deep end stairs in there because my understanding is that you need at least a ledge in the deep end so that swimmers can exit the deep end. So, unless you plan to put a ladder in, it makes the most sense to leave them in, or at least put in some form of ledge for deep end egress. Bummer about the trencher going through the drain line, but I agree that you can probably just replace the line from where the pipe was damaged. I'm always nervous about trenching given all of the plumbing in the ground in our yard (esp. the gas line and 60A/220V line that is dedicated to the pool equipment). I don't think you will need to main drain line too much. In our case, the line to the drain is rarely used.
As for the term "cleaner line," I meant that if you want to install a dedicated cleaner like a Polaris or Zodiac, it's really nice to have an extra pipe plumbed to the side wall of the pool where you can hook the cleaner into. There are several different kinds, primarily vacuum, pressure side or robotic. The former is the cheapest way to go typically. We have a Zodiac MX8 that is suction side and we really like it. It is plumbed into the suction manifold of the main pump, with a three way valve controlling suction between the skimmer and the dedicated vacuum "cleaner line." As I've added a leaf catcher inline with the automatic cleaner, the only maintenance is removing leaves and debris from the basket in the leaf catcher once every week or two. Alternatively, pressure side cleaners typically require a "booster pump" that is plumbed with the return of that pump driving the pressure side "cleaner line." This option is more expensive due to the booster pump. But, you could in theory use the same cleaner line plumbed either for vacuum or pressure type cleaners. It's your choice once you have run a cleaner line to the pool. It's not an absolute necessity, but it can really help reduce your time maintaining the pool. Lastly, there are robotic cleaners, but these are expensive. However, they do not use a dedicated cleaner line, so if you forgo adding this additional plumbing, you could still equip the pool with an automatic cleaner. You might check out the Automatic Cleaner forum for more details.