I've done that once for a 386SX, which was on a PCI board. A good source on how to start a X86 cpu in protected mode is the source code of linux. It's just a few assembly statements. After that you can use gcc to compile your C code. The result is objectcode in ELF format. I wrote my own linker, to make a program out of the objectcode. And yes, it worked! Good luck.
