So, I'm getting to to a point where I may be riding this bike after I got a bunch of bugs out. The muffler, which I presently have off the bike sounds like it's got a ton of rocks inside of it rattling around. Is there a way to fix this or have the baffles just fallen apart inside? Also, I see where people restore their bikes to almost new...I understand repainting and such but finding new parts is almost impossible anymore...how do you guys do it??

I bought an aftermarket expansion chamber for my DT400 that was cheap because the seller said that something came loose inside the pipe and was rattling around when you roll the pipe from end to end.

I went ahead and bought it. It turned out to simply be a huge mud dauber wasp nest that was inside the pipe and came loose allowing it to tumble around inside the pipe. I used a plumbing drain snake to crumble it into small enough pieces to dump out the open ends of the pipe. 

So maybe you have a mud dauber wasp nest in yours too!

I was able to look inside the end of the muffler with a flashlight and it's definetely a kind of metal baffel that's come loose. Can't get it out of the end of the pipe though...
 

Not sure when you say “muffler” if you are referring to the removable spark arrestor on the end of the exhaust or if you are referring to the main exhaust pipe itself.

The link below shows what the inside of the removable spark arrestor looks like when cut open. I believe there was also post long ago that showed what the inside of the exhaust pipe looks like when split open.

imgur.com/a/PWkUU4O
 

That's a different looking muffler...yes there are two pieces, I'm talking about the one that hooks to the jug and bolts under the seat. The other end slides into the large muffler and bolts to the side panel on the left side of the bike. The large muffler end is what I'm talking about. What's rattling inside is a round perferated pipe with a screen wrapped around it. It will not fit through the end of the muffler to get it out though...
 

Hmmmm.
It does sound like your innards have come loose. I know what I would do. Ride on and worry about other things. You can come back to this issue when all others have been resolved and you are looking for something to do. If you didn’t shake the exhaust you wouldn’t even have known there was an issue.

LOL, well you're right about that! Isn't causing any other issues and I'd have to cut open the muffler to get it out..