It's good that it's running, now you can get onto the cosmetics.
The four valve engines had issues with header pipes cracking at the collector. I had a K100RS that had 3 exhaust systems replaced on warranty before the owner finally put a Remus system on the bike. I suspect that is probably why yours has that enhanced safety(loud pipes save lives) system on it.
Good exhaust systems are around on ebay, and if you can't find one for a four valve engine, it is possible to use a two valve exhaust system with a bit of fiddling with the mount. I did that with one of my bikes and it worked pretty well.