"it" refers to his shirt. "it probably was" means "his shirt probably was crawling with fleas", though, oddly, substitution of this does not create a logical sentence.
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GPYthough, oddly, substitution of this does not create a logical sentence.True, if you include 'crawling with fleas'. In that analysis I think we might say that 'which' is to be taken as 'and', though I must say, Clive has an ingenious solution to the problem that leaves 'which' as 'which'.