Does anyone know where to find a good bootloader for the mega2560 (fe from adafruit) ?
the 2560 uses a different bootloader than the 328-based arduinos, and I don't know of any crafted alternatives.
But I need the full hardware memory capacity (as it is a large sketch with a lot of variables)
"lots of variables" is irrelevant to bootloader issues with large AVRs. The 328 bootloader (based on stk500v1) doesn't handle flash memory pointers larger than 16 bits, so it's limited to AVRs with 128k or less of memory (64k words.) But the existing MEGA bootloader implements stk500v2, which includes support for more than 128k. The 8k bytes of RAM usable by variables is pretty much a drop in the bucket.
I don't see any support for WDT in the stk500v2 bootloader; is that all you actually need?