The only custard recipe I have is for rice custard. Suppose you could drop out the rice for plain custard. I suspect the 1% milk is the culprit for your watery result. That will certainly cut down your fat content but not sure how much it will really cut out the carbs. Here is the recipe I use minus the rice.
1 qt milk (I use whole milk)
3 tbsp melted butter
1/2 tsp salt
2 c sugar (since I do 'no flour/sugar' I'd probably use splenda here)
3 eggs beaten
1 tsp vanilla
1/2 tsp nutmeg
Mix all together and pour into a buttered 2 qt casserole (can probably get away with smaller casserole as the rice is not adding to the bulk) and set into a pan of hot water. Sprinkle with more nutmeg. Bake at 350 for 1.25 - 1.50 hours. May need to adjust the cooking time as well, again due to the rice not adding to the bulk. If you decide to, the rice for this recipe calls for 1 cup of cooked rice.
It makes a delicious rice custard. As mentioned, I follow the 'no refined flour/no refined sugar' diet. Changing out the sugar to splenda would be the only change I would make. In fact, might do this one day this week. Haven't made it for quite a while.