Had to figure out how to post the full error first....
C:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM9 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m
avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch
System wide configuration file is "C:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"
Using Port : COM9
Using Programmer : stk500v1
Overriding Baud Rate : 19200
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 : STK500
Description : Atmel STK500 Version 1.x firmware
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us
avrdude: AVR device initialized and ready to accept instructions
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)
Error while burning bootloader.
Reading | ################################################## | 100% 0.02s
avrdude: Device signature = 0xffffff (probably .avr8x_mega)
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.
avrdude done. Thank you.
Schematic of my board is too large to embed here, can be found at: http://www.kbob.org/Pictures/Artsy/Other/Other/USBuino.png
Though is basically a copy of a pro micro with a few extras.
The MAX3421E is not powered during the attempted flashing process.