Flattening will just make it look good, but does not do any good for the soil, in fact when you remove the top soil, it does more harm than good.
What are the problem that you may face if its untouched, fix only those issue, If you are facing any issue like water logging its worth fixing only those area.
My feel is that for drip irrigation you can use the gradiance in a good way, my field is does have elevation of about 30ft, i plan to use it for gravity fed irrigation.
Usually vegetables will be grown on raised beds, practice in your place may differ, for this levelling is not required.
For trench, could you get the software to find the contour lines?. Did you try SketchUp?