Hi Vince,
When you mentioned “I had a page that offered a check box for Exchange and Lync”, do you mean the page as below? 
If so, you can still check the boxes and use the related services in current Office 365 subscription. Enterprise E3 contains several kinds of services, and it’s not able to split these services and assign them to users separately.
If anything is misunderstood, could you please explain the situation more clearly? I will do my best to help you.
Regards,
April Zhou