Due to the requirement of footprint compatibility with the PDIP version of ATTINY85 the board cannot be smaller than 0.4" by 0.4". Unfortunately I was not quite able to get there in this spin of the board. It is still 72 mils too long.
For all the large components I use the same as Tim did. Diodes, resistors and capacitors are what I had in my parts bin.
When looking at the original Nanite 85 board it is obvious that the through hole pin headers take up quite a lot of space. On the other hand I was not sure if SMD soldering the pin headers would be solid enough to withstand repeated extractions from the breadboard. I finally ended up doing something in between.
The holes are drilled most of the way through by hand. The pin headers must be shortened and filed a bit but eventually they fit. I the slide the pin through the plastic rail and solder the header to the PCB like this:
Now it is just a matter of sliding the plastic rails back in place and solder the top side components.