I've helped lots of SaaS companies improve their onboarding processes over the years, but I just published my best (high-level) piece on doing this right:
http://sixteenventures.com/customer-onboarding

The bottom line is (though I suggest reading the entire article) you need to know what success looks like for your customer - what their Desired Outcome is - and then reverse engineer the steps necessary to get there.

Going through that process will reveal the steps necessary to get them to that Desired Outcome outside of the product; we're not talking about functional steps within the product yet. Map this out using flow charts, line lists, mind map, white board, etc. The tool isn't important as much as doing this right.

Now, once you understand the process required to move them from Step 0 - deciding to take action to reach their desired outcome to Step z - achieving their (at least initial) Desired Outcome, you can start laying out, designing, and building the in-product processes necessary to achieve those success milestones and ultimately, their Desired Outcome.

You should then peg your email (or other lifecycle messaging) flow to those success milestones (rather than doing a timed follow-up), where each message is sent like this: "have they done this milestone? yes, then send this message to get them to the next one."

Since each user and customer will achieve success on their own cadence, it's best to not have a timed autoresponder sequence but to actually trigger based on milestones reached. The good news is that this is relatively easy to do given the availability of lifecycle messaging services. See this post for more on this topic:
http://sixteenventures.com/email-follow-up-sequence

Hopefully this helps, but if you want more details or - more importantly - want to figure out how to apply this thinking directly to your situation, request at least a 15-minute call with me.