You put your firmware in and click download ropbin. It doesn't go up to 10.4 though, only 10.3.
Unless that is the wrong thing and it's just this part you need to do
Blank image display at boot
If you want to hide the image display so it won't display junk or "the menuhax loader", you want to place this imagedisplay.png at /3ds/menuhax_manager and then configure image display within menuhax_manager.
Removing chunks of code in a payload that requires precise timing to run properly - and even when finetuned it still has a slim chance of crashing - is always going to impact boot rate in one way or the other. Things like these are extremely finicky - sometimes even the smallest change will prevent them from booting at all.