Arudino Bootloader/Code on other ATMega chips?

Other Hardware 3rd Party Boards
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I've been looking at taking my Arudino Uno based project to a custom PCB for a number of reasons. One of which is I've run out of flash memory for handing both an SD card and LCD. I suppose I could use an ATmega2560/V chip like in the Mega board, but then I'm looking at 100 pins or so which seems a bit more complex. The AT90USB1286 has only 64 pins and plenty of flash/ram for my application and has direct USB connectivity.

AFAIK, none of the existing Arduino boards use the AT90USB1286 or any chip from that series, so it is unlikely that I could just use the Arudino bootloader. Is that right? Honestly, I'm not 100% positive what the bootloader does- or if there are other ways to run code built with the Arduino SDK. Looks like the Teensy++ 2.0 board uses this chip and it sounds like it's from a software perspective compatible with the Arduino?

Hoping someone can point me in a direction of a FAQ or HOWTO which explains how to move code which was running on an Uno board to something like the AT90USB1286 or if it'll never work and I should just plan on learning to solder a 100 pin SMD part. I'm pretty familar with Makefiles, compilers and I'm not afraid to drop into a shell to get a build environment working- I'm just at a loss right now what path to take. Seems like I need a way to get the boot loader installed and then program it?

Thanks!

-Aaron

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I think it would be significantly difficult to move arduino code to an AVR with built-in USB. If you were planning on still using the serial-like interface on the PC side, you'd have to figure out how to do the USB processing "concurrently" with the sketch itself. Maybe. Check with the usbtiny code to see how they handle it?

There is the mega640 (64k of memory) and mega1284 (128k of memory) that are only 40 pins, and available in DIP.

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Looks like the Teensy++ 2.0 board uses this chip and it sounds like it's from a software perspective compatible with the Arduino?

In my experience the Teensy has been fairly compatible but I'm not using an SD card or an LCD display.

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Sounds like the ATmega1284 would be a simple drop in replacement. And if I didn't want to learn SMD I still have a DIP option too. Sweet. Thanks for the replies!