Downside of the Wiseco piston is they jump in 0.5mm increments, meaning you might only need a 1st over 0.25mm re-bore to clean up, but you're forced to go to 0.5mm, reducing your number of potential re-bores.
Positive of the Wiseco pistons is they go to 2mm over, which I'm not sure the Yamaha piston does.
If it were mine I'd ask them to hang on, measure the actual bore and see if you can get a 1st over Yamaha piston.
This is all assuming it will clean-up with a 1st over re-bore.

As a green horn with this exact topic, my head is spinning.. It seems "only" experience can tell what you need to do or not... I'm not a fan of hauling/sending stuff off to be determined whats the next step.. I wish there was a guide to lead the beginner... 
Honing.. boring and pistons... (here's where sneezles61 tips over) 
Sneezles61

Amen, brother! 

I too like to do my own work or source it locally, but found shipping my CT2 jug off to Enduronut was worth the peace of mind knowing that it would all come back with the minimum overbore necessary, tight tolerances and an oem piston.

Put a couple thousand miles on it since then, so I did hone and new rings this year, that felt comfortable enough done at home.

Quick update, I was able to catch them before they ordered the Wiseco so we're on hold until I hear back from Enduronut. I emailed using our contact form but if anyone has a better way to reach him I'd love to know. Maybe he's away on vacation.

I don't know if saying "search forum for his email" is not clear enough. This might help.  yamaha-enduros.com/index.php/forums/fng-...les-and-parts#108590

I'm sure he gets enough spam without having his address posted here every day. 

And for those asking for beginner advice on boring and honing it's been on this forum many times.  Used a trusted professional who knows what they are doing with these old bikes.  Not that easy to find on your own.  Nor is it easy to tell what piston you need for an overbore without sending out your cylinder to have it measured and checked by someone who knows how and follow factory specs. The difference of the thickness of a human hair in clearance tolerance can make the difference between a job that last a long time and one that rattles like hell...  or worse... seizes...  Not to mention proper chamfering, etc. 

Some jobs are best left to experienced professionals. 

Not to say that you "must" always bore and hone...  there are some quick and dirty techniques in many threads here that talk about getting a ballpark idea if you're "close enough" on a used cylinder and piston for a budget job... these old bikes are pretty tolerant.  But if you're going to get it bored it's worth doing it right the first time.  Many horror stories of botched jobs on here. 

Adguy, it takes a bit of time before Enduronut to respond. He is a very busy Man.

   It’s been a while since I posted anything on this CT3 rebuild. I was able to get the piston and rings from a enduronut as well as some clear and calming advice. I also watched some step by step precise you tube videos from a channel operated by Dale Sweger who hails from Montana which I highly recommend to anyone who has yet to do a full rebuild. The bore and crank rebuild took longer than I like to get back but eventually It arrived and todayI finally received the last missing part to complete the engine work and start the break in procedure. It started after a few kicks and sounds great. I only ran it until it fully warmed up. Can’t wait to continue the process and move over to final cosmetics. While the ratty bike only cost me $400 I invested around $1400 in parts, machine work and supplies. Thanks to all who helped me along the way.