Here is the layout:
Here is a possible generic exposure of ATMEGA pins:
Here is a realization. Please, note that flipping the 1000Pads Mini Breadboard you have to reverse the power strips (+ and -) with respect to the previous layout schema.
And here is the Minimal Arduino running the blink example (the ATMEGA chip is on two stacked IC sockets).
Power is coming from a simple 5V regulator based on 7805.
Please, note that this implementation takes the schematics from this official standalone version, but it has a strange wiring of AREF pin to VCC(+5V). This should be avoided (accordingly to ATMEGA328 datasheet) and, in fact, official Arduino schematics does not have such a connection, and adds a 100nF cap between AREF and GND for noise reduction when using analog input pins. You can refer to this new post for a more correct version.