Will adding 1M (legitimate/correct) internal backlinks to an orphan page trip algo penalty?

[DrewProZ]

We have a massive long tail user generated gamification strategy that has worked really well.  Because of that success we haven't really been paying enough attention to SEO and in looking around caught some glaring issues.

The section of our site that works as long tail goes from overview page > first classification > sub classification > specific long tail term page.  Looks like we were relying on google to crawl/use forms to go from our overview page to the first classification BUT those resulting pages were orphaned - so www.mysite.com/product/category_1 defaulted back to the search page creating duplicate issues.  www.mysite.com/product/category_1  and www.mysite.com/product/category_2  and www.mysite.com/product/category_3 all had duplicate content as they all reverted to the overview page.

It's clear we need to make an actual breadcrumb trail and proper site taxonomy/linkage.  I'm wanting to do this on just this one area first, but it's a big section with over 3M indexed "specific long tail term pages".

I want to just add a simple breadcurmb trail in a sub navigation menu but doing so will literally create millions of new internal backlinks from specific term pages to their sub & parent category pages.  Although we're missing the intermediary category breadcrumbs, we did have a breadcrumb coming back to the main overview page - that was tagged nofollow.  So now I'm contemplating adding millions of (proper) backlinks and removing a nofollow tag from another million internal back links.

All of this seems in line with "best practices" but what I have not been able to determine is if there is a proper/better way to roll these changes out so as to not trigger an algorithm penalty.

I am also reticent about making too many changes too quickly but these are SEO 101 basics that need to be rectified.  Is it a mistake to make good improvements too quickly?

Thanks!

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