Electronic – Micro-Controller Programmable Selection

This is one thing I could find.... http://www.sparkfun.com/products/10549 It might not be exactly what you want, but Sparkfun is glad to help and answers quite quickly. The community will also help you if you need much help. Most of what you need in that kit is already included (From what I can see). If I find any more I will edit this answer.

This sounds like a job for embedded Linux.

1. Persistent file system. Forget IDE (save yourself 40 pins) and go for a board that uses a flash card.
2. More RAM and Flash. Typical embedded Linux boards have RAM in the megabytes.

As for peripherals, driving 40 servos could be a question here on its own. How are you doing this now? For the rest of your peripheral requirements, here's a board that seems to fit that has a good community as well:

http://beagleboard.org/static/beaglebone/latest/Docs/Hardware/BONE_SRM.pdf

The tool chain has a C++ compiler, it has SPI, UARTs, and even a PWM. This is what's being claimed in the PDF at least, you'll have to make sure that there are drivers for all those peripherals available to you at the application level for whichever distro of Linux that you put on. Hopefully the one they provide has everything you need.

So basically, if you can port whatever you've written to a Linux PC, there's a good chance you can port it to an embedded linux target. However, I'm willing to bet that if all you're using from C++ is <fstream> and <string>, you could probably do a C re-write and save yourself the overhead of Linux.