This is how I approached this problem-
My takeoff run is limited. So, depending on my configuration I calculated the maximum possible velocity I can attain in my groundroll. I assumed that at the end of the run my lift should be greater than the weight I want to carry. So I computed the lift I generate at the end of the groundroll. I got the CL value from xfoil for my angle of incidence. Would this method give me a rough estimate of the total weight my plane can carry?
Yes, you can do your equations at OEM (Operating Empty Mass) and get your ground distance. Then you can calculate the same for different mass values (your OEM+your payload), and generate a distance vs mass. Since you know how much distance you have (including any safety factors), you can see what mass you can take off with. Or work backwards from the same equation, set the maximum distance you allow, and work back to your mass value.
Keep in mind this will not tell you whether the airplane is structurally strong enough to carry that weight, only if it can take-off with it. Structural calculations are a bit more complex than this. Also, you might want to do similar calcs for landing distane as well!
How did you calculate the maximum velocity achieved in ground roll, without knowing weight on board? It seems unlikely that your approach is going to lead to a realistic estimate of how much weight you can safely get off the ground from a short runway-- I think you are going to need to find some performance tables based on real-world data, or create your own.
IF your calculation of max velocity at end of ground roll was somehow correct, then your approach MIGHT lead to a very conservative estimate of how much weight you can safely lift. The reason for this is that you appear to be basing your calculation on the fuselage being in a level attitude, not nose-high relative to the flight path -- (you said "for my angle of incidence".) In other words you appear NOT to be basing your calculations on the MAXIMUM lift coefficient that your airfoil can achieve. But not knowing all the details of your calculations, it would be impossible for anyone to really give a reassuring answer to your question.
