MicroC/OS-II on FreeDOS - Recycling PC's as Embedded Controllers

I am starting a new project that re-tasks old PC's as embedded controllers. To start with I am using motherboards with integral serial and parallel ports; USB support for FreeDOS is out of my reach (temporarily).
I am using an Arduino Mega2560 as the I/O processor via the hard serial port.
My goal is to have multiple PID controllers running as separate tasks on multiple cores (or Hyper Threads) controlling real hardware in real time.

But first steps first: Currently I boot FreeDOS on a PC without hard drive, floppy drive or CD-ROM, just using a USB Thumb Drive. (Most BIOS's these days support USB devices at boot like keyboard, mouse and USB thumb-drives)
I have tested the Open-source μC/OS-II RTOS and the example programs work just fine. Here are the particulars of the lab machine:
Motherboards: ASUS P4C800E, Gigabyte GA-MA785GSM-US2H
Memory: 4GBytes, 8GBytes
Processors: Pentium 4 Dual Core, AMD Athalon II Quad Core
Video: AMD Fire Pro AGP card, Integral motherboard Video

Boot OS: FreeDOS
Development toolchain:
Compiler/linker: DJGPP GNU based C/C++-compiler/linker/libraries
NASM Assembler in 32Bit Protected mode.

What I am looking for is some help devising a debugging scheme to view what is happening on the target machine.
Is anyone interested in working on the project with me?

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