Any exhaust gurus out there?

I have never had the correct exhaust on my 83 XJ650. The one it came with has the "box" instead of the crossover pipes, where the 4 downpipes become 2. In order to fit a sidestand, which the bike was missing when I bought it, I had to cut apart the box and widen it, and now it sits cockeyed and the downpipes don't fit too well into the front...
So then, I found a set on eBay that appeared to have the right 4 -> 2 arrangement, though I have not been able to figure out exactly what they came from (they have a Yamaha part #, are all black, and the mufflers are not tapered).
So now I am in the process of installing these. They go on in halves, that is, you install the right side and then the left side, and connect the two (front and rear) crossover pipes in the process.
Now the rear crossover pipe, which is just at the front of the mufflers, absolutely and totally intereferes with the centre stand. So, I cut it off, and intend to close off the holes. (I have no alternative if I want to fit this system, which I do, as it will make room for saddlebags.)
My question for the engine tuners is: is there a risk of a serious loss of performance? If we're talking one or two or five percent it won't bother me, but if the bike will barely fart along I may as well cut bait now and save myself some time and aggravation.
I have a rough idea of how these things work, balancing pressures, scavenging, etc, but am also aware that it's a science. My guess is that the front crossover is much more significant but I don't really know why I think that.
I hope this is going to work out as I do like the look of the system too. I just wish I had a digital camera but not yet.
Thanks in advance,
Jim

 

Well I got lucky!
After much cut, fit, fiddle, trim, grind, fit, over and over and over.....I got it finished tonight. (The left half of the system also interfered with the sidestand so I had to re-route the pipe around it.)
So regarding holes that remained when I got rid of the rear crossover pipe, I just closed them off, and hoped for the best.
Wow! The bike performs much much better; I am quite pleased. I have no idea what I have done really, but it goes to show that the exhaust system can make quite a difference.
I used to have quite a bog around 3000 rpm, but now it pulls evenly right through to about 5000 rpm (didn't try faster), with maybe a small bog around 2500 - but nothing compared to before.
A side benefit is that it sounds cool, kind of British I think. And I will be able to fit saddlebags - but first I will be changing the seat.
This bike will look all different from when I bought it last summer. Lots of fun though.
Jim

 

Sometimes it's better to be lucky than good