Hey Scootern,

I'm up for the jetting challenge and already have a set of main jets ready to test out.
I will look up where I got the seat from. I can't remember off hand. I have build thread in the customs forum for more details on the fitment.
The Husky is a 2015 TE 350 that I use 100% off-road for trail/enduro riding. Sadly it has not been ridden much for the last few months.

Seat came from here. classic-motorcycle-fiberglass.com/contact.htm based in Australia. 
I had to have it padded and covered. Then I painted it. 

Had some time to ride with the new exhaust today. The jetting I had proved to be too rich. 
a couple of sizes smaller on the main jet made a huge difference. 
It's running well and rides well but is not quite making as much power. It doesn't lift the front wheel off the power in 1st as it used to. 
Doesn't hit power band as hard and doesn't hold 100km on the hills it used to. 
Still some more jetting to try out before I investigate further.
 

Do you think the baffle in the muffler is too restrictive causing needing to reduce jetting like a carboned up baffle--same effect.

Could be. I will clean up and try the other baffle that I have. Maybe even take it for a short ride with no baffle.
Other considerations, the header internal dimension being smaller could be an issue that will not be easy to overcome.
There is a baffle inside the chamber that I would assume affects the the performance too

I am surprised that their is no packing in these mufflers. I am used to fibres packed around the core

Ok, i'm surprised too if there's no packing but only if it looks like their should be as some where the gas zooms in & out have none but fit close all the way through separating plated to divert the gas. I'm sure ya know that so ignore me. The one i ran was off an LC350 so the first model 250 350. But i also ran that pipe on my vmx bike RT2 or mixture of parts but had an RT2MX top end & originally i ran a DT1MX pipe which worked ok--but--when i ran the LC pipe it fair transformed it & pulled from very low down but revved to the moon & made super strong power all the way. Wish i had some pics of those days. I don't think i cut the main chamber up so don't know what was inside it, but had to alter the header a bit like you did.

Today I tried the 2nd baffle that I have. Slight improvement in power. Then I removed the baffle entirely. Huge improvement, but way too loud for me.... I'm old....
Off the bottom was a little weak pulled through the middle and then hard up high. I move the clip on the needle to a richer position and even better results. 
So it runs much better without the baffle but is too loud. Could probably even run better with some jet work. 
What to do next?
I am thinking about cutting it open and removing the baffle inside the chamber and/or removing the inner core in the baffle. 
Thoughts?

I thought the baffle would be easy to pull apart by cutting through these welds. I was wrong. 

A couple of ideas. 
The muffler has 2 compartments as per this pic. 
I could trim the end off the baffle to remove the most restrictive part. 
This would mean shortening the baffle to approx 160mm in length. 
The other option is to keep trying to remove the end of the baffle and remove the inner core.