The silencer shouldn't have a noticeable effect while riding, regardless of how it's packed.
A stock 250 has more than adequate ports to utilize a shearer pipe, it wouldn't cause a loss of power.
When you get it running right you'll want to give that FMF away so you never have to think about the possibility of using it again.
Problem with switching pipes is that they need different jets...so it'll be harder in a way to narrow down the root of the problem.
It could tell you something if the problem persists with both pipes, and that it's not an issue with the pipe itself...but who knows for sure?
Keep toying with the jetting, keep going rich until you KNOW it's way rich, then back down until it starts getting better.
Be cautious when it starts running real good, because you're probably dangerously close to being too lean.
At that point, start doing plug chops and get it dialed in to a safe main jet.
A few other things, try running it without an air filter to see if you're getting too much restriction and check to make sure you're getting adequate fuel flow.
Make sure your carb is clean and the float level is correct.
Start running consistent fuel and oil, every time...mixing race fuel and pump gas isn't a great way to get consistent jetting.
About the only thing left after that are the reeds and ignition components.
There's a lot of different things it could be, you just have to start eliminating them one by one.
I had a similar issue with a hybrid that ran a TMX-38.
Nothing was wrong with anything on the bike, but I couldn't get the jetting right.
No air leaks, ignition was fine, plenty of fuel flow, no intake restriction, no detonation, compression good...the carb just didn't want to take a tune.
No matter which way I went with the main jet, it would always bog down under full throttle.
I got it so rich that it fouled the plug on a full throttle run, and I backed down one main jet size at a time until I got to the point where I was leaving white residue on the plug (too lean).
Nowhere between way rich and way lean did it run without bogging down above 7/8 throttle.
So I just ran it rich on the main to be on the safe side and never gave it more than 7/8 throttle.
Got to Glamis (big elevation change) and had to re-jet...managed to get it indicating rich on the main and rode for about a tank of fuel before it burned a hole in the piston.
Came back, did a top end on it after leaving it to rot and hold various other projects I was working on for a few years, replaced the TMX with a stock carb and the bogging never came back.
The TMX is probably still out there somewhere melting pistons and collaborating with the owner to develop new derogatory slang, I wouldn't know...I sold that stupid thing and would have been happy if the dude gave me a stick of gum for it.
I know it doesn't have a whole lot to do with your situation, but sometimes BS just pops up without any reason at all...even if everything appears to check out good.
You'll figure out the problem eventually, hopefully in less time than it took me
