Don't really have that much more to add to what has already been said. It's a difficult balance to strike because our priorities are different - academia is all about discovering new things, software engineering is more about getting things done according to specifications.
The most important thing I can think of is to try and extricate yourself from the culture of in-house development that goes on in academia and try to maintain a disciplined approach to development, difficult as that may be in many cases owing to time restraints, lack of experience etc. This control-freakery sucks away at individual responsibility and decision-making and leaves it in the hands of a few who do not necessarily know best
Get a good book on software development, Code Complete already mention is excellent, as well as any respected book on algorithms and data structures. Read up on how you will need to manage your data eg do you need fast lookup / hash-tables / binary trees. Don't reinvent the wheel - use the libraries and things like STL otherwise you are likely to be wasting time. There is a vast amount on the web including this very fine blog.
Many academics, besides sometimes being primadonna-ish and precious about any approach seen as businesslike, tend to be quite vague in their objectives. To put it mildly. For this reason alone it is vital to build up your own software arsenal of helper functions and recipes, eventually, hopefully ending up with a kind of flexible experimental framework that enables you to try out any combination of things without being to restricted to any particular problem area. Strongly resist the temptation to just dive into the problem at hand.
