So here is my story...

I recently had a new piston put into my bike, and was taking it out for a good break in session. This was maybe the 3rd or 4th riding session I had gone on since picking it up from the shop, and so far it was riding really awesome. This time however, I was not so lucky. A few times on the ride I would suddenly lose power and my RPMs would drop. When I tried to give the bike more gas it was almost as if it were either choking it or flooding it because my RPMs would drop even more and my power would greatly decrease. But as soon as I pulled the clutch in the RPMs would shoot up. So I decided not to go any further away from home, and turn around. It happened to me a few more times on the way home, so I decided to take a loop close to my house to try to replicate the problem so that I could call my mechanic and explain to him what was going on. Well, I rode around for nearly an hour trying to duplicate the problem with absolutely NO SUCCESS. Does anyone have any idea what it could be? My mechanic did tell me that I had rust in the tank that needed to be cleaned out, but I have owned this bike for nearly 2 years and have never had an issue like this before. I thought maybe it was jetting, but wouldn't that happen all the time? Thank you for your help!

Do you have a fuel filter installed?
If not, there's a chance your carb ingested some crud...

Probably the most important question here is why a piston replacement was required, the new one may be in grave danger !
Pictures of the piston that was replaced, info from your mechanic as to what he thought had happened, your history of problems related to this etc, etc
When asking for help keep typing background info, it’s almost not possible to give too much background info and pictures if you want to go straight to solutions

I had somthing similar happen to a 74 DT360A that I had converted to points ignition. Hemibusa, a highschool buddy and I were heading to the Grand Canyon. Total loss of power for a bit then back to normal. Then it died and wouldn't start. No spark. We did what we could but no success. When home after checking alot of things I found the wires going to the condenser had come lose under the solder. I was lucky that I found the issue.

I had to replace the piston and re-bore the cylinder because the engine seized. The engine seized because I'm a dumb and didn't check the oil before going on a ride.

I do have a fuel filter, in fact it is brand new. But maybe something could have snuck by it?

as you have a filter, may be more likely that the crud blocked the fuel supply, by slowing up or pulling clutch in you gave it a chance to refill the float bowl? maybe a quick check of fuel flow out of fuel tap and the filter in the petcock bowl

Checked the gas cap, be sure is venting correctly, or remove it while it happens, at least to eliminate the cap. I had a similar but not quite the same problem on my DT360.

Had a similar issue on a CT-2. I opened the main jet holder and let a little gas flow through to wash something out in case it was stuck. Started right up and ran very well after that. Something to try if it comes up again.
My brother (who has many, MANY more hours on bikes than I do) and I were riding a pair of my bikes out in the Idaho forests at the time. I really looked like I knew what I was doing even though it was just a guess!

My fuel filters have a flow arrow on them. Not sure how they work if they are backwards......