I'm not sure why your limonene is cloudy, but if it was cloudy before the sodium carb wash then I would recommend you just continue with the process as you would normally. If there is some impurity in there causing the cloudiness, it shouldn't precipitate when you salt with fumaric acid so I wouldn't worry about it.
How long did you leave the distilled water sitting in the limonene? Water washes on alkaloid-containing solvents should be as quick as possible. Add water, shake really well, separate layers. Even still, I doubt that any of your DMT was left in the water. If you are really concerned about it, just add a small amount of limonene to that darkened water you used for washing, mix well, pipette the limonene off, and combine it with the rest of your limonene. This would retrieve any DMT that had somehow made it's way into the water.