Durria,
I recognised the name but I was not sure it was you.
You need to take advice from WHO (and others) about taking, labelling, storing, and transporting the specimens. I would have a nurse or phlebotomist in each team to draw blood for anything more substantial than a pinprick. Sharps and the risk of infection will need strict policing. I would use a reference lab. If you use a local lab then validate a subset of results with a reference lab making sure the local lab knows that this will happen.
With S3M we tend to estimate or classify for small areas. This require use to have reasonable large samples from each PSU and, for national surveys, many PSUs. In the planned S3M I think there will be about 3000 PSUs with 32 HHs from each PSU. If we assume that there will be 1.5 children per HH then the overall sample size will be about 144,000 children. To include them all in the micronutrient sample will be very expensive. What you can do is to calculate a state level sample size and try to get that as a subset of the S3M sample from each state. If (e.g) you had m = 1OO PSUs in a state and a required an overall sample size of n = 400 then you would need to sample n = 4 children from each PSU. Since you have many small clusters the design effect will likely be very small. If you have staff limits then you may want to take n = 15 children from m = 30 PSUs. I would advise not to go much below m = 25 PSUs from each state. As the number of cluster drops and the within-cluster sample size rises you may start to see substantial design effects.
You need to make sure that you can assign each specimen to the S3M PSU number. That will allow analysis by state and by region and overall.
I hope this helps.