EDIT4:- Here's an overview of what I'm doing now.
First I choose a single light source out of multiple using simple heuristic scheme like the distance, intensity, area and the cosine falloff angles. I appropriately set the weights for the light like this
$light\_pdf = weight/area$
where weight is in range 0-1.
Next I trace the ray to see if light source is visible. If it is I calculate the $light\_sample$ using the direct lighting equation (integral over Area).
Then I calculate the BRDF PDF for this given ray. However I use Lafortune's algorithm for it. If a random number falls under the specular color I sample through the modfied Phong PDF else through Cosine.
The weights are computed using power heuristic, $ weight = light\_pdf^2/(light\_pdf^2+brdf\_pdf^2)$
The MIS estimator is then calculated as
$light\_sample = light\_sample * weight/light\_pdf$
After that I come to BRDF sampling. I again sample through either Phong/Cosine based on what I did earlier during light sample calculation. If the sampled ray doesn't hit any light source or not the same one. I set the $brdf\_sample$ to zero. If it hits, I set the $light\_pdf$ to same value as before. Calculate the weights like mentioned above and calculate brdf sample using the original equation (integral over solid angle).