Haggis ... That GS1000 should be a nice project. When I take on these project bikes (I also have 3 restored CB750's), I just take it one step at a time and keep my work relatively organized. It's easy to get discouraged if you start thinking about all the things that need work.
This is actually the second GS1100E model with V&H pipes that I've tuned up. My friend has exactly the same bike, but it ran very poorly and the header pipes were totally burnt dark blue and brown. I followed the rejettting recommended by V&H in stages ... main jets first, along with the airbox mod. Bike ran much better, but still was a fair bit of backfiring/popping on deceleration. Then I changed the pilots ... and that helped a fair bit more ... but still a bit of popping was evident.
So, I actually upgraded his air jets from (I believe) Canadian model OEM 140's to 160's. The 160's were in the carb rebuild kits we purchased. Following this change, his bike is now running perfect. I think my bike still has the OEM 140's ... but since it's running great now, I'm leaving well enough alone.
Unfortunately, his V&H 4 to 1 single walled header pipes are already badly burnt up cosmetically (the cows are out of the corral). Putting that freer breathing exhaust system on, without rejetting, resulted in a very hot/lean condition. I'm hoping that with the proper jetting and "Blue Shield" internal coating, my new headers may well stay relatively good looking. Blue Shield has certainly saved my CB750 Custom from a similar fate. It has 17,000 kms on the aftermarket single wall headers, and they still look like new.
In case you're interested, here's a couple of photos of my new V&H headers ... after I coated them with the Blue Shield ceramic paste.
The product is very easy to apply, and well worth the extra effort when installing new single walled header ... at least in my humble opinion. Good luck with your projects.
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