I've worked in finance and operations for two eCommerce companies and worked in consulting as a data analyst. I've faced similar problems where data is spread across disparate systems making a high-level view of the business difficult.
Unfortunately, I don't know of specific tools that would aggregate data from accounting systems, customer databases, CRM, etc. In the past, I've built custom dashboard applications in addition to managing a collection of spreadsheets, SQL queries, and third-party reports.
In eCommerce this is maybe a little easier than in other industries since many of the tools we use have APIs to build on top of. It's also probably not cost effective to build a custom solution until you have well defined processes and metrics that you're already comfortable with.
For forecasting and modeling, I'm not aware of a better solution than Excel. The process is generally very iterative and qualitative, and Excel provides the flexibility to create models specific to the drivers of your business.
For most small to medium sized business, the tasks of managing spreadsheets, creating dashboards and reports, and building forecast models can generally be handled by a single skilled Business Analyst. This would be someone who had both technical ability and business acumen.
I'm happy to go into more details about processes and solutions that have worked for me in the past or make more specific recommendations if you provide a little more detail about your business and your goals.