The chip I had placed on by JCLPCB, also how do I change the clock to the internal 8Mhz, COM port is detected and the traces seem fine. The other board I tested on was a clock I tried to make and it works fine, never have an issue bootloading. I also tried making a solder joint for J1 on my USBasp in order to slow down the SCK line, but that didn’t work either.
Here’s a picture of the back of the board for context.
As regards too the clock speed I set up that within ‘tools’ in the Arduino IDE what you are using right ? but I am running out of ideas now because I can’t replicate any of this at home. Did you check for the clock running and reset condition ? I think it’s time to use a dedicated forum, any of the Atmel/Arduino forums will probably walk you through a set of steps instead of clutching at straws like I’m doing 
for instance I have never used USBC is that set up correctly ? is that even relevant ? so not sure what more I can do.
You board looks really nice!
I just finished a project that uses those same multi-color LED (Neo Pixel, WS2812, WS2811 and SK6812 LED/drivers) and when I went to have the boards made the manufacturing house told me the datasheet recommends those parts be baked at 60 degrees C for at least 24 hrs prior to relow oven soldering them. This bakes off any moisture that can damage the parts when they are soldered in the reflow process. This added time and cost to the board maufactuirng as I had to upgrade from the basic standard PCB assembly process to the Advanced PCB assembly process. I dont know if this would apply to hand solder too. I didn’t know about this when I was designing my project and it would have influences which LED I used. I thought I’d pass that along as info…
I am using the Arduino IDE, the RESET line is high and gets pulled low when I hit “burn bootloader”. The programmer is set to USBasp, the board is set to Arduino Leonardo, Clock on the scope did not show any output despite changing crystals, and changing caps from 8pF to 22pF. Already asked this question on the Arduino form but nobody seemed to answer, along with r/embedded on Reddit. This is just kind of frustrating cause like you said it’s a simple process and should work. Also, USBC did work on my digital clock board, its simply tied to D+ and D- on the Atmega32U4. what Atmel forum would you recommend?
Thank you! I just can’t seem to get it to bootload, its a really cool project but I can’t actually upload my code right now.
Oh ok, How to run without a crystal is in the datasheet of the chip somewhere. Is that a 8 or 16 MHz oscillator ? and is it a resonator or a crystal I haven’t used that package. Ok, first thing is to establish the clock is running at the PIN on the IC if it isn’t then you start there if it is then good. In the meantime a site I used regularly is ’ AVR Freaks’ type that into google they are the AVR/Atmel guy’s go check that out.
Gotcha, here’s the digikey link: TSX-3225 16.0000MF18X-AC6 EPSON | Crystals, Oscillators, Resonators | DigiKey and its a 16MhZ crystal, I tried checking pins 1 and 3 on my scope, on the clock board which works the signal would rise to around 3v (can’t remember exactly) but on the bad board it stays at 0. Also when probing the good board with a scope, probing the clock makes it fail to bootload or upload code, so it seems pretty sensitive. That’s only when I probe it though.
Ok does the good board use the same crystal ? According to the data sheet the load caps can anything from7pf up so it isn’t that. The good board will probably not work when probed because the probe itself will load it up so don’t worry about that you need to get the clock oscillating on pins 1/3 so check voltages are all present at the chip then check the integrity of al components around your crystal as this must be the problem.
To read the chip signature the chip does not need a CPU clock !
This is a programming interface issue.
drtech, you need to spend some time reading the reference manual for AVR processors and the datasheet for that specific chip. go read them.
The questions you are asking - that information is all in those documents I have suggested you read.
Also, read the docs on AVRDUDE programmer, which I think that is.
Mousy, the programming speed is nothing to do with the baud rate of the com port.
Will do, I have read the datasheet before, although I found it rather confusing, especially given the fact that I designed the board the same way before and it had no problems.
there are multiple datasheets to read. the chip reference manual and programming manual are necessary reads.
anyway, like I said, if you cannot read the chip signature, then you have a programmign interface fault / problem. forget the board clock for the moment. (or you have counterfeit chips )
Does your programming setup work on another board ?
I would suggest take these questions and this topic over to microcontrollers at EEVBLOG, you’ll get more relevant assistance there.
The programming setup on my failed digital clock works with no problem, same MCU, same crystal, load caps, reset switch, and everything. Could it possibly be that the MCUs JLCPCB soldered onto my boards are bad chips?
Thanks for that, but what I said was " usual programming set up is 9600 baud check your on the right ‘COM’ port. " Which is standard Arduino check list, so I stand by it and there’s no need to get all technical with the guy as its clear he is learning as am I. In fact as I’m typing this the OP just said as much. You can read an AVR MCU with no crystal running ? I didn’t know that cheers! if you read the comments he has also said that he does have a working set up in his last comment in fact.
Appreciate you and everyone else trying to help, really just wanting to get this board to work.
Bad chip Is a possibility yes but would say unlikely however at the moment it could be anything, I didn’t that you don’t need a working clock to talk to an Arduino, but all the Arduino problems I have fixed on my own projects (clock related) have been external clock not connected or internal clock not selected, As far as I’m concerned you need the oscillator on your board to work if you don’t fix it now you will have to do it later anyway because the MCU wont work fully without it. 
Well, we can rule out that the USBasp header isn’t working, nor am I missing anything in terms of connections or parts so that either leaves an improper layout or a bad chip if MISO MOSI and SCK read 0V on the bad board and rise to 3V on the good one. At least thats my thought process on it.
I can’t count the number of times I faced Bootloader problems with Arduino… many times.
Most often in was the Arduino IDE and specific version/release and next, it was Driver for the Clone Chip/Board.
I used many Atmel chips and never bothered to set Fuse’s and Bootloading is a well-known hiccup… Try using the correct Programmer selection and if it doesn’t work, try Avrisp mkII
Then, next was the Arduino settings (mostly USB speed but, other issues too…)
Happened so often I learned to fix it in my sleep (I use a lot of Clones) - I suggest you check with the Arduino forum but, first check the compatibility of specific Chip/Board and Driver…
ADDED: Also try the ArduinoISP selection - I use that for my homemade programmer
Indeed it is an Arduino right of passage 
Our OP isn’t using Arduino as ISP his working set up is using USBasp.
I remember there was always 2 versions of the Arduino Nano bootloader, and forever and a day the one that worked was (Old Bootloader) great fun.
I have about 30 old Chips and Devices (Nano and Uno) that need the OldBootloader.
I have about 20 newer one’s that can only use the New/Current Bootloader…
Yes, a Right of Passage 
Just noticed the back of your completed board and have a quick tip
Place the JLCJLCJLC text under a component. That way it is not visible. The AVR looks like a nice place to hide it. Remember that the text can be pretty small so it would probably fit under it.
Just makes things look a little nicer,
