| Turn off the tank lights. Close any nearby curtains. Change about 75% of the water but take your time topping off. If you have a PH test kit compare the tank water now to what comes out of the tap. Hopefully it's the same. If it is you should be able to match temperature and go ahead and refill the tank. I like to hook a hose directly to the sink so I can adjust hot and cold to get a match. If the ph in the tank has crashed compared to what's coming out of the sink then fill slowly over a period of time. This would also be a good time to get your gravel back in or other desired substrate. With your fish load you'll something to provide more space for bacterial growth which the gravel will provide. In addition I don't know of any way possible for aquarium bought gravel to contribut to green water.
This one change by itself will not remove all of the green since you're leaving at least 25% of it in the tank. I would suspect a clearing though to maybe a dingy shade. With the light sources blocked your tank should gradually clear though. If it doesn't within a week or so, repeat and look for alternative light sources like room lighting nearby. If it does clear then gradually start using your tank lights again. A timer can help to limit the hours the lights are on. If it greens up again due to the tank lights then you may need to change bulbs, reduce bulb quantity or change lighting types. If it doesn't green up then try opening the curtains again. You may have found the culprit in direct sunlight which is the most common reason I've had to go through this in the past. If that's the case then leaving the curtains shut permanently or repositioning the tank or adding another piece of furniture in between may be needed. I had one guy who went through this for months before he finally found direct sunlight hitting the filter which spray painting the body black resolved.
Also watch the ammonia and nitrite for any spikes. You removed the gravel so you may have removed enough of the bacteria bed to create a short term spike.
Long term be prepared to thin the tank load. Shubunkins should grow anywhere from 8 to 12 inches long and the koi can reach up to 3 feet or more. Way to much fish load for that size tank unless you hope to stunt their growth.
Good luck. | 
Help! Dying Goldfish 
