I had a previous thread https://www.wristtwisters.com/#/topics/80019. I replaced the tank, fpr, pump, all fuel lines, and spark plugs. My idle is set between 11-1200. The only other thing I did was add a Speaker led headlight. So.....I got it all back together, filled the tank with ethanol free and seafoam, and went for a ride.

When I first give it throttle in first gear, it has like a “chatter” and the exhaust sounds really throaty before it goes into the power band, otherwise it ran fine. I jumped on the interstate and it was running ok, no one around, so I opened it up a little. At around 90, I shifted into 6th, got to 100 and then no matter how much throttle I gave it, there was no added power. It sloowwllly climbed to about 110. It didn’t bog at all like before, but I don’t really know where to go from here.

Is your tank venting correctly? Next time you go for a ride and it starts bogging, pull over and carefully open the tank cap. It should open quietly. No suction or movement of air.

I went through things today, there is no vacuum issues with the tank. It rides fine, it just won’t go over 110 even with the throttle buried. It’s like I’m getting no power in 6th. It shifts in solid. I did replace the tie rod between the shifter and pedal but the spline is at 11 oclock and it shifts through all the gears

Perhaps dirty injector/s from all that rusty crap. There is a basket mesh filter/screen in each injector.

My ZX10R did that. I replaced the fuel pump after thinking about if for quite sometime. Cured.
Just a thought.
Good luck.

I changed the FPR a few months prior to replacing the tank and pump. Should I change it again? Is there anything to clog in the FPR, or should I just clean the injectors

You can't clean an FPR. If it's new it should be good.
You did remove to black rubber transit bung from the main port before bolting it down?
Before pulling the injectors check the plugs. They may show which injector is playing up.
Inspect your injectors for obvious blockages.
The best way to clean injectors is by taking them to professionals. They'll test em too.
Before going to the effort of removing your injectors eliminate everything simple first.
Check your plugs, coils, wiring etc. Recheck the fuel delivery system, all your recent work etc.
Feel the headers when the bike first fires up, to be sure all cylinders are heating equally.

I know I can’t clean the fpr, but could I have ruined it using it with the crap tank?

My bad, I misread your post. I got it in my head you had asked about cleaning the FPR.
I wouldn't have thought you could have ruined it. As long as fuel is running through it it should work. Can you see if the fuel return hose is doing what it should?
Just to eliminate you could replace it.
Is your fuel pump a new OEM?

Brand new oem pump assembly and return hose. I took the fpr off today just to make sure I hadn’t been drinking when I installed it and all looks good. The exhaust smells like unburnt fuel. It was acting worse than ever yesterday, super jerky and sputtering in first at take off, almost didn’t make it home. My battery light flashed once and my Speaker headlight was strobing everytime I took my hand off the throttle, so I started thinking it was battery related...like maybe the pump wasn’t getting enough juice, battery tested 13.11

Fuel does shoot out the return side of the fpr with the bike running. I don’t know what it means, but cylinders three and four get alot hotter, faster than 1 and 2, but they eventually even out.

With fuel in the return line I'd say your FPR is fine.
OEM fuel pump should be fine.
All four headers should heat up equally. So somethings not right there.
You should check your plugs. Is there a difference between all four?
I don't think it's coil related since one coil runs plugs one and four and the other coil two and three. Yet you say headers one and two are slow to heat. Does this mean they aren't getting enough full? Perhaps.
Injectors one and two are at the "dirty end" of the common fuel rail. When your bike is on its side stand leaning over the fuel rail is tilted down, any crap in your line will settle down that end, at one and two. I'm thinking injectors one and two are dirty.
Check out the last couple of posts in this thread... First two cylinders not firing Help https://www.wristtwisters.com/forums...ad.php?t=29366
Just make sure your plug leads are fine too.
My bike sat for years before I got my hands on it. It had a rusty tank, filters full of a fine red crap, like mud. Bike still ran OK? But after I stripped it down I found the mesh strainer basket on injector full of the same red crap.

So, I finally got sick of messing with it, called the local Honda dealer and they told me to bring it in. Managed to make it there ( bike actually was great up until the last 3 miles) and when I got there, they said they didn’t have the expertise to diagnose it (and tried to sell me a 500). Called the only other Honda service center around and they won’t touch it either. They said (without looking at it) it’s probably a piston. It’s going to get the injectors cleaned at a mom and pop place and if that doesn’t work, here comes an MT09 or Speec Triple

I tested the battery at 13.11 and running at 14.4. The spark plugs look lean, but it’s running at low end like it’s flooding. My guess is a stuck injector. Today, all cylinders heated equally except 3 heated up twice as fast

Maybe 3 heats up fast cause it's running lean. Lean for hot, rich for cool. Perhaps the no.3 injector is partially blocked causing a lean condition.