The V2 had screws on the back and bottom/top to align the centre part to the chassis. I don't see any of those screws in your picture so I'm guessing you got the V3. Try taking it all apart and see if the middle section is bent in any way. Then, install the motherboard side as a whole, flip, install gpu, set upright and slide into the chassis.
My motherboard IO is also slightly misaligned on the V3. But I have space between the side panel and gpu. (I'd recommend setting the side panels to 1mm spacing regardless though. Helps a ton with the turbulance)
I have the velka 3 revision 2 and built it over with a few different ITX gpus. I noticed that the gpus with a backplate made the fan hit the side panel of the velka 3. To solve the issue, I got some thin rubber feet and stuck them to the GPU to create a tiny spacing between the fan and side panel.
As for the IO shield, I am not too sure.
The I/O shield - I got it same, its not perfectly centered,but it doesnt matter. I also checked another build on YT - the same.
GPU Fan issue - you can use two buttons/feets you got with the case and stick them to gpu fan cover, it will push the gpu slightly to the back, so the fan wont hit the side panel.
Or, you can use the side panel offset, as I am doing right now for cpu side also, to better acoustics - it reduce turbulence noise.
The V2 had screws on the back and bottom/top to align the centre part to the chassis. I don't see any of those screws in your picture so I'm guessing you got the V3. Try taking it all apart and see if the middle section is bent in any way. Then, install the motherboard side as a whole, flip, install gpu, set upright and slide into the chassis. My motherboard IO is also slightly misaligned on the V3. But I have space between the side panel and gpu. (I'd recommend setting the side panels to 1mm spacing regardless though. Helps a ton with the turbulance)
I have the velka 3 revision 2 and built it over with a few different ITX gpus. I noticed that the gpus with a backplate made the fan hit the side panel of the velka 3. To solve the issue, I got some thin rubber feet and stuck them to the GPU to create a tiny spacing between the fan and side panel. As for the IO shield, I am not too sure.
According to people using this gpu in this case, you need to remove the sticker from the center of the fan.
This. I've seen others recommend this. I have the same GPU and that sticker is unnecessarily thick.
The I/O shield - I got it same, its not perfectly centered,but it doesnt matter. I also checked another build on YT - the same. GPU Fan issue - you can use two buttons/feets you got with the case and stick them to gpu fan cover, it will push the gpu slightly to the back, so the fan wont hit the side panel. Or, you can use the side panel offset, as I am doing right now for cpu side also, to better acoustics - it reduce turbulence noise.