If you just need a system to get the exhaust gases from the front of the engine to the back of the bike, any old system will do that OK.
But if you want performance, it will need to be tuned to your bike.
I've done a bit of research in this area and tried to get my head around exhaust system design. I learned that optimum exhaust header length is dependent on cylinder phasing (180° or 120°), cylinder volume, revs at which you want the power peak to come in, valve sizes, valve timing, and a few other parameters. Then you have to consider header diameter, collector size and length, muffler or megaphome type and design. It all gets too complicated to work out mathematically. So most performance exhausts are designed by trial and error, mostly error.
What I'm trying to say is that the random 2nd hand 3-1 system you've bought may not be optimum for the performance of your particular engine. It's much more likely that it won't work as well as the factory exhaust.
You may be OK with slightly reduced engine performance if you're just riding around on the street at legal speeds, but keep an eye on fuel mixtures. If it runs lean you could do some damage to the engine. You might need to re-jet the carbs.