Too many homepage links?

I have a website about 2 years old. I made the mistake of buying PBN links (as well as building my own links) and sending everything to the main homepage and NOT the inner pages. October of last year I got hit with the penguin 3.0 update but have since had that penalty lifted and recently started link building again. I am now ranking on page 1 for half of my big money keywords, but the homepage isn't even the one that is optimized for each of the terms. My page 1 rankings are sitting #4-#9. Will building more links to inner pages using these anchors help? Should I dilute the hell out of the homepage links by building up inner page links, but keep link building for those terms directly to the home page? I'm confused on how to proceed. Note: not a churn and burn site.

Are you banned from Google? If you are then you should start over with a new domain

No. I have good rankings now. I incurred the penguin 3.0 penalty back in October, but mid December the site recovered and has a lot of page 1 rankings again. I've been building links again and climbing higher in the serps, but I'm worried about all of the links being pointed to the home page.

Does your homepage contain relevant content for your target keywords or your internal pages?

OP, I have a simple answer. Build links only to pages that are getting traffic. If your home gets 60% of your traffic then it gets 60% of links. You CAN'T build links to a page that has zero views. If you have to buy a few views to the pages and then build a few HQ links. You can't just suddenly blast pages that no human has ever read or G will notice.