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Here the authors study matrix functions introduced in the first part. Basic properties of the principal connection matrix \\(G= G(x\\mid \\alpha_ 1)\\), \\(x= (x_ 1, x_ 2)\\), are given. This matrix function depends only on \\(x_ 2/ x_ 1\\). The formula is presented relating \\(G= G(x\\mid \\alpha_ 1)\\) with \\(G= G(x^{-1} \\mid \\alpha_ 1^ \\prime)\\). The special cycles \\(\\text{reg } Y^ -_ i \\otimes Y^ +_{ n-i}\\) are defined which are connected with \\(G\\). It is given the asymptotics characterizing them. The cycle \\(\\text{reg } Y^ -_ i \\otimes Y^ +_{n -i}\\) is expressed as a linear combination of \\(\\text{reg } Y^ -_{j, n-j}\\) and \\(\\text{reg } Y^ +_{n-i, n-j}\\). Explicit expressions for the coefficients are given in terms of theta monomials. Matrix elements of the matrix \\(W_{\\tau_ r}\\), introduced in the first part of the paper, is expressed in terms of the connection matrix for Jackson integrals of the function depending only on \\(x_ r\\) and \\(x_{r+1}\\). 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