I am working on a dataset of 41 items on Likert scale supposed to represent three latent variables (an independent(28), mediating(5), and dependent one(8)). I collected 450 responses and performed an EFA on it as a first step to conduct CFA and SEM. The results of the EFA revealed 7 factors having eigenvalues greater than one, with the items of the independent as well as the mediating variables are loading on the same factor. In addition, 3 items of the dependent variable loaded on the second factor and three other items loaded on a third factor. How could I deal with this situation, given that I will not be able to combine the independent and the mediating variables together in a single variable, because the three variables are already placed in the research title. Thank you.

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