USB upload to Pro Micro (32u4) My project is based around the ATMEGA32u4 microcontroller.  

I followed the Arduino Pro Micro schematic to design my own board layout and build a custom PCB, soldered on the components.  Then I used the Arduino IDE to successfully upload the Arduino bootloader with SPI.  

Currently I can also upload programs to my `32u4 over SPI (using "in-serial programming").  Tested that with Blink.  

But I cannot upload programs with the USB, like you would normally be able to do with a Pro Micro.  What things should I look for to debug this?

avrdude: Version 6.3, compiled on Jan 17 2017 at 12:00:53
     Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
     Copyright (c) 2007-2014 Joerg Wunsch

     System wide configuration file is "C:\Users\Myname\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino9/etc/avrdude.conf"

     Using Port                    : COM12
     Using Programmer              : avr109
     Overriding Baud Rate          : 57600
     AVR Part                      : ATmega32U4
     Chip Erase delay              : 9000 us
     PAGEL                         : PD7
     BS2                           : PA0
     RESET disposition             : dedicated
     RETRY pulse                   : SCK
     serial program mode           : yes
     parallel program mode         : yes
     Timeout                       : 200
     StabDelay                     : 100
     CmdexeDelay                   : 25
     SyncLoops                     : 32
     ByteDelay                     : 0
     PollIndex                     : 3
     PollValue                     : 0x53
     Memory Detail                 :

                              Block Poll               Page                       Polled
       Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
       ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
       eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
       flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
       lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
       calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
       signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

     Programmer Type : butterfly
     Description     : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .avrdude: butterfly_recv(): programmer is not responding
The answer, as kindly pointed out by Gerben, is that ISP program upload overwrites the bootloader.  

Only upload the bootloader via ISP, then switch to USB for uploading Arduino sketches.