This circuit stays a bit more compact by having the DS1307 RTC breakout soldered directly onto the Pro Trinket 5V. This makes the reset button on the Pro Trinket 5V more difficult to access, but you can still enter bootloader mode by using tweezers to push the button or just by unplugging and plugging the Pro Trinket 5V into the USB port. When the Pro Trinket 5V first powers up, it will be in bootloader mode.
You don't have to do this, it simply makes the circuit assembly more compact by using A2 and A3 as power pins (The DS1307 is powered by turning A2 low and A3 high in the Arduino code.) You can also just freewire the RTC breakout.
DS1307 Real Time Clock breakout board
Start by assembling the DS1307 Real Time Clock breakout board by following this learn guide. You only need to solder in the male headers for GND, 5V, SDA and SCL. You can leave off SQW since it isn't used and the header won't fit nicely on top of the Pro Trinket. If you do solder it in, you can clip the bottom lead off.
Once the DS1307 breakout is assembled with headers, you can solder it on top of the Trinket Pro 5V so that the DS1307 GND lines up with the Pro Trinket A2, 5V with A3, SDA with A4 and SCL with A5. Make sure the boards are lined up correctly! SDA and SCL need to be connected to A4 and A5, respectively.
Solder the DS1307 RTC board onto the Pro Trinket 5V and then clip the excess leads.
NeoPixel NeoMatrix 8x8
Connect the NeoMatrix GND to the Trinket Pro GND, 5V to 5V and DIN to Pin 8. Cut the wires 5-8 inches or 13-20 centimeters long. Solder the wires into the back of the NeoMatrix so that the wires won't be visible from the front.
Here are the connections into the Pro Trinket 5V:
And this is what the finished circuit should look like!