Crate engines vary in use. I've see the x engine come with fox, sn95 and even explorer parts. The main thing is the long block. Trade the covers to someone for stock foxbody covers.
I'm surprised there isn't clearance issues with the TB, many times tall covers need an intake spacer which is also prone to causing a vacuum leak if not done properly.
Most cold air intakes on a fox are crap, other than Anderson ford power pipes. The
bbk is metal, which get's hot. I wouldn't put it on the priority list, but I would ditch it.
Look for used 24's and you will need a pro m or pmas meter meant for 24's. It will have to be a meter meant for a fox, the cheapest and most common is the bullet, used they are around $100. Make sure the calibration is for 24lb injectors.
The meter helps control the mixture, this could be why it runs so rich.
Take a picture of the top of the meter sensor.
Nothing on the car is terrible, but it does show signs of just being slapped together with random parts.
It's not going to take a whole lot of money to get right.