Are there any best practices that I should follow while writing a parser?
Don't overuse regular expressions - while they have their place, they simply don't have the power to handle any kind of real parsing. You can push them, but you're eventually going to hit a wall or end up with an unmaintainable mess. You're better off finding a parser generator that can handle a larger language set. If you really don't want to get into tools, you can look at recursive descent parsers - it's a really simple pattern for hand-writing a small parser. They aren't as flexible or as powerful as the big parser generators, but they have a much shorter learning curve.
Unless you have very tight performance requirements, try and keep your layers separate - the lexer reads in individual tokens, the parser arranges those into a tree, and then semantic analysis checks over everything and links up references, and then a final phase to output whatever is being produced. Keeping the different parts of logic separate will make things easier to maintain later.