Warning: I am not an electrical engineer. So, everything here is probably wrong. What little I know, I have taught myself.
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Step 1. Breadboard the components
Set everything up on a breadboard and ensure the circuit works
Step 2. Cut 10-pin Female header
The fan needs a 6 pin female header, but I only have 10 and 20 pin headers.
With a box cutter, firmly, gently and slowly cut most of the way through one side, on the end that is not needed. Try to cut parallel to the black plastic divider between pins. You want to keep the divider intact, because it acts as a shield.
When one side is cut, flip it over and repeat. When both sides have been cut, then slowly cut one side and then cut the middle row, again slowly.
If you don't have ridges, then you probably made a mistake. Sand down the ridges on the cut end with 80 or 100 grit sandpaper
Step 3. Snip off GPIO 24 pin from 6 pin header
The pin isn't needed, and gets in the way of routing the 3.3v wire
Step 4. Orientation
Because of the fan, the protoboard must stick out from the side of the case. Be sure to orient the rest of the work accordingly.
Step 5. Flip the components
This is the part that drives me nuts.
The breadboard is upside down when compared to the protoboard. To place the components correctly on a prototype board, the components must be flipped upside down.
I find it less error prone if I make a simple drawing of the breadboard and then do an upside down drawing of it. In this case, I also rotated the S8050 to make routing of the wires easier.
Once everything is placed correctly, count the rows and columns of holes. The one that worked was 3x7.
Step 6. Cut Protoboard to correct size (row by columns from above)
Cut the protoboard slowly with a tin snips. Fast cutting, or long cuts will make the board break or flake
Sand the edges of the protoboard so they are straight. I am a slob, so straight is very subjective.
Step 7. Insert the components
Insert the components and route the wires.
Component go on the side without the gold rings, and soldering is only done on the side with the gold rings.
Use Bostik Blu Tack to hold components in place
Step 8. Solder the components
I start with the unused header pins to give it some stability
I follow this guide when soldering
Step 9. Using a dental scissors, cut the excess leads