To answer question 3, you should have been told which NCBI build you data was set to, and for mteh most part if the SNPs were genotyped recently, the build should be the most recent build.  I you cannot find the build information in any of your raw data files, I would suggest finding the file that has the SNP name and it's coordinates and then do a search in dbSNP.  You should be able to find the correct build based on the coordinates given in your file.  For example I just looked up the SNP rs2661837 in my file and my file says the coordinate for this SNP is 160,790,174Mb on chromsome 6...i searched for the SNP in dbSNP is says that my data is using build GRCh37.p13.

As for question 2, you need to look at the "Final Report" files you have.  In these files you should have several columns including ones called "Allele1 - Forward" and another called "Allele2 - Forward".  If you use those columns for your allele calls, your alleles should all the ones on the forward strand.

Hope this helps.

Erin

Regarding Q1. 1000 genomes data are in forward strand, you can compare your alleles to 1000G to check they match. Take care with A/T and C/G SNPs where the strand is ambiguous. If you extract from 1000G a population which matches your own then allele frequencies can be used to double check that the alleles are matching correctly.