Install everything but the GPS and Si5351 when programming the Atmega328 to avoid applying too much voltage to them.The Atmega with my programmer uses 5v,the GPS and Si5351 will not handle that,they are only 3.3v max.Best to play it safe.
(Be sure to set your ATmega328 fuses for 3.3v operation,continue reading this post)
(Using your saved .eep configuration from your U3S kit,see last section video below)
Once programmed,solder in your Si5351 and test that it will transmit.Yes,it will be off time...etc,but best before soldering the GPS module.
NOTE - In the programming section,when you setup your U3S for modes and bands you are going to use,save the EEPROM to your PC where you can later transfer to your payload Atmega328.Command line used for me to SAVE eeprom is "R" to READ to PC and "W" to WRITE to your Atmega328.Simply change "R" and "W" in the command line for this.
Commands based on programmer and methods used (example) -
avrdude -c usbtiny -p m328p -U eeprom:w:.hex:i (r or w)
Add the 1uf capacitors to voltage output of each regulator.I had also added a 1uf to the INPUTS of the regulators as well.Using the 0805 caps,they are very small and do not add much weight.All caps are grounded from both input and output voltages to eliminate RF issues.Carefully plan where to place the caps and scrape the PCB to a convenient ground.
Battery voltage can be added if you want to monitor this by adding 2 resistors.One 3k and one 6k.Since the board version does not accommodate pads for this feature,add them in by simply laying them on the board as not to short other components.One leg of the 6k is grounded by scraping the PCB.Both the 3k and 6k are soldered together (end to end) and using a jumper wire to PIN 26 of the Atmega328 between both resistors.The remaining leg of the 3k is a jumper going to your power source where it will detect voltages providing your firmware is capable.
Double check my notes FIRST to be sure I have this correct.Ask questions here on the forum to be safe.
See the attached image for these modifications (below).It can look confusing so look it over carefully.
GPS ANTENNA is a 45mm wire directly soldered to the PCB GPS antenna pad.
Experiment using fewer solar cells of around 3v and test in full sun without a battery.I have not tried this using the board but it may operate this way thus eliminating extra weight using a battery.
Finally...take care when soldering the Si5351 IC chip.After destroying several,they appear to be very heat sensitive.PCB pads can be easily pulled from the board as well if over heated.Do not use a hot air tool for these chips and double check your hand soldering carefully.
S+ is solar input to blocking diode.B+ is battery input with "G" as ground.If battery is not used,connect solar to B+ directly and do not use blocking diode.Running another board using the SOT23 works for me directly from only 6 solar cells (3v). Experiment yourself to eliminate battery weight.
The last firmware I have used for flight was 3.10a.You can setup for WSPR,but to receive altitude and ground speed,JT9 is used.I am sure other firmware version will work the same way.I am sure the firmware in your current U3S will work fine.