The Custom ROM has several apps and features that I will remove and settings that I will set (just like any other ROM) This wouldn't be a big issue if I wouldn't flash a rom every few hours
So how to custom install a custom rom?
Unless the ROM is specifically designed to allow some kind of default set-up (and I don't know any that are), you can only do this by building the ROM yourself from source. You can edit the build scripts to remove any apps or features you don't need, and the source code to change the default settings, then compile a ROM image yourself.
You don't say why you're flashing a ROM every few hours. Obviously if you're flashing different ROMs, changing the source each time is going to be harder than just setting the settings on the device. If it is essentially the same ROM you're flashing each time, then you can keep your settings across flashes by simply not wiping the userdata partition when you flash the new ROM. Bear in mind that if the ROMs are significantly different, this may make the new ROM unstable, because it's trying to use settings files that were written by the old ROM.