On my current set up I’m getting better results with less latency between takes. Meaning for example when I track one guitar part and lay down another they are much more closer in time than on my older set up. But, there still is some latency. I see that waves InPhase is on sale for $29, so I was wondering it it would be worth gettting? I know this isn’t really what it was designed to do, but since it’s really about shifting timing around to ache I phase coherence, wouldn’t it work? Or, is there a different plugin that would do this better?

Thanks all.

Have you tried CbB Audio Snap tool? That's what I would use. You could get as precise as you would like. Take both trks and enable Audio Snap on both. Then with the little lines you see move the parts that are not in sync closer together. Depending on what the wave form looks like, you can just sight it in. Or if you can't see the different section, just move the audio and listen back. 
 
You might be able to use Vocal sync to achieve the same results on smaller sections. But depending on how far out of sync they are, I don't think In-Phase would move the wave in time enough.

You're barking up the wrong tree trying to fix sync issues after the fact. Assuming you're using your interface's zero-latency monitoring correctly, the real problem is more likely due to incorrect latency compensation. 
 
A DAW needs to know what the latency is so that it can line up the takes correctly after recording them. Sometimes, the interface doesn't give it the right correction value and you have to set a manual offset so that everything comes out properly lined up.
 
Somebody once posted a good step-by-step procedure for setting the manual offset. Try googling "site:forum.cakewalk.com manual offset". If you can't find it, check back here and I can describe the process.