You are doing a great job
They are a very much under estimated bike for EVO.
The rear mount of the exhaust that you can see on top of the stinger section above the airbox (last photo) attaches via a rubber mount to a bracket on the frame. The bracket appears to be missing on your bike. It is located on the right hand top rail about 20mm behind the cross tube. I will get some photos of my VG which is the same for you. The bracket has a tendency to crack if the exhaust is not mounted correctly or the head steady is loose causing bad vibration.
The rear silencer is available as a reproduction. The last one I purchased came through John at Rocky Mountain Montesa. There are three size silencers you need the longest one. The 250/360/414 reproduction silencers fit 250s as well as the big bores you just trim the last 20mm or so off which has a reducer to fit the smaller and shorter 250 chamber. They are good quality.
The link that connects the brake pedal to the brake cable/rod is a piece of flat metal about 18mm x 3mm bent into a work of art that passes behind the frame and under the swingarm. A photo is the only way to show you so will try to get one ASAP. Not sure if Jared from South West Montesa or John from RM Montesa can help. If you contact them I'm sure they would have a new one or possibly a used one.