Dimar I'd also check your php timeout settings in configuration. 5000 products is really not that many. I've successfully used Easypopulate for over product loads upwards of 30,000 at a time.
I'm unclear as to what you are trying to do though, you want to share everything including categories but not products? Obviously with multisites cat_filter functionality it is simpler to place segregated products in diffferent categories and then restrict those categories to certain sites.
However if you are only doing 1-2 sites I generally think it's better to just have seperate sites honestly. The work to setup and maintain multi-site will be more that just operating seperate stores. I'm only considering it because we will be running more than 100 template sites and obviously there will be economies of scale there.
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