Problem of Porting Flash Programmer.

What do you mean by you "leave the clock and reset pins unassigned"? I'm not familiar with the Microtronix Dev. Kit, but your Flash Programmer design (created by mk_target_board) doesn't have any chance of working without a clock and reset. You need to hook it up, just like you would for any other NiosII-based design. In fact, depending on your board, you may even need to add a simple delay reset circuit (like in the majority of the example designs), as well.