So i have a scenario where the recording engineer used overhead mics to record left toms and cymbals with 1 Mic, 1 Mic for the center toms and cymbals and 1 Mic for right toms and cymbals. Has anyone experienced this situation and how did you approach it? So far I've left them as is however I could see where cloning the tracks, EQing and gating might separate the sound and be beneficial. What has been your experience or thoughts? Thanks

Using OHeads to get the full kit sound is a fine way to go.  Make sure the mics have the bottom end to cope with the toms though.  I have never used a centre mic in the OHead setup though, not really necessary.  You will always need a kick mic because the OHeads will never capture the kick properly.  It comes down to whether you are also using a close mic on the snare.  Something your post has not mentioned.  If you are then, I tend to set up the OHeads as a spaced pair thing and either side of the kit and not getting as much of the snare then.  The close snare mic will take care of the snare sound.  If you are not using a close mic on the snare then a co incident pair of OHeads will work nice too and just a kick mic then 3 channels is all you need. 
 
I still feel micing all the drums and OHeads is best and gives you the best options overall.

My apologize, I did not mention all other drums had their own individually mic'd tracks. It was only on the upper toms and cymbals where they were mic'd together. Before i started experimenting to see if it sounded better I was curious if anyone had tried cloning tracks that combo'd the toms and cymbals to try and add better separation or if it was not worth the effort. Yes I know its subjective so looking at people who have tried both approaches and their thoughts. Thanks

I've cloned overheads to separate toms. I make one clone for each tom, get in close, listen to what's being hit and when, chop up the hits and add fades. After cutting the clip(s) for each tom I use Slate Digital Trigger or Addictive Trigger, find samples that work, tune them to match the overheads and mix to taste.
I've never used three overheads when recording drums, it sounds like a phase nightmare to me. X-Y has enough separation, saves set up time and is fool proof for this fool.
Shure KSM 32s are highly regarded for full kit overheads.
 
Rocky
 
 

X-Y Overheads OR Overheads spaced both work fine.  For the spaced OHs, I like to point them directly at the drums, equal distances from the snare to prevent phase issues.  I have recorded drums using several mikes one for each drum and separate one for high hats,but usually only end up using the OH, Kick and maybe the top snare for a little more snap.
 
 

What kind of mic's did the engineer use.  If they were sdc's then maybe cloning the tracks is an option.  If they were ldc's or ribbons then cloning might not be necessary as there  might be enough low energy in the track as is ...
 
How do the toms sound?
 
I agree with the comment above about the phase issues.  Can you drop the center track?
 
Another option that may take a bit of time and patience but might be worth it if it is a great take but the toms are not cutting it ... is to use drum substitution software and use the take to create individual tracks for the toms. Once you have the substituted tom tracks the focus on making the cymbals sound great.  You can do this with individual samples too and just build the tracks manually.
 
 

Update: After getting the SSL E plugin from waves I added it to all my drum tracks. What a huge difference it made on the acoustic drums. I then tried the cloning of the 3 overhead mic's. On 1 set I chose the tom preset in the SSL and on the cloned set I chose the overhead preset. Fortunately I did not get any phasing issues. As a result I'm now running my acoustic drum recordings as the predominant drum sound as opposed to the triggered AD2 drums which initially sounded better. What a difference 1 plugin made.