Why must you use the same number of beads when you construct the second chromosome in step 1?

You should use the same amount of beads for both chromosomes because they need to match in size.
I am assuming you are making a pair of homologous chromosomes out of pop beads, and they should have the same size because they code the same information, the only difference between them is that one comes from the mother and ther other from the father. (Homologous chromossomes have the same genes in the same loci).