Reddit mentions of Marketing Metrics: The Definitive Guide to Measuring Marketing Performance (2nd Edition)

I started an e-commerce company right before the dot-com crash (we launched in 2000) so I feel you.

As for what metrics to track, it really depends on your specific industry and how you run your business. If you can't get your books and CRM to talk to each other (odd since they're by the same company) I'm sure you could export data and crunch numbers in Excel.

Since you work off leads I would dig down to try to find data on some of the following questions:

• What was the average time to close a lead April 2015? Did it increase or decrease in April 2016?
  
• How do you track leads? Is it effective and accurate?
  
• How do you qualify leads? Could it be possible that even though you're getting 20% more leads, the quality of the leads has gone down? Look at the source of the leads (marketing, search engines, sales calls) and see if something has changed in your targeting, marketing, audience, etc that correlates to the change.
  
• Do some research into your customer trends. Create segments for customers that generate $25-50k profit a year and for those that generate < $5k profit. Look at the differences between the two. Are the # of leads in the 2nd group increasing and the 1st decreasing? Why? Make changes to target efforts on leads in the 1st group.
  
  Those are just some thoughts off the top of my head. As for resources, you might get some value out of reading The Lean Startup and Marketing Metrics.