So this is the best fix I can come up with for the moment, and I use the term best very lightly.
First let's go over what's required:
1. Firefox or Chrome
2. A Gmail account
So first things first turn on notifications for a thread (with this jury rigged method I would suggest only doing notifications for one thread at a time.) You will find this option at the top of threads you have created.
As seen in the pic (sorry I used a thread that I already have notifications set up for, normally it will say "Notify"
Step 2: Download the Gmail checker app for Chrome here. https://chrome.google.com/webstore/detail/google-mail-checker/mihcahmgecmbnbcchbopgniflfhgnkff
And Firefox here https://addons.mozilla.org/en-US/firefox/addon/gmail-notifier-restartless/
These extension will allow there to be a Gmail icon with notifications for how many emails you have. As seen here.
So what I like about this method is that when I turn on notifications for a thread I can see when I have replies without actually checking my Gmail constantly. I just look up there see that I have some unread emails and assume that it's replies to my thread. It's by far not the best way and I doubt many people will want to do this but I like it and think it's the best method at the moment.