mswyka, I have been on this site long enough to know that you absolutely know what you are doing....
This Intruder is not running like it should.....many good suggestions already mentioned.
I will throw this out there...since you have already examined the drivetrain and all seems OK.
Is it possible someone has substituted an Invader tuned pipe on your Intruder sometime in the past?
The earlier Invader pipes were very similar in appearance to the Intruder pipe.
An Invader pipe, designed for around an 8000 RPM power peak would make an Intruder (7000 RPM) fall flat on it's face.(and vice versa).
This is why I like gixxer's suggestion to substitute components from your good running Intruder....1 at a time.
The frustrating thing as you have been troubleshooting this problem is that it is probably something pretty simple.......substitute components from your crisply running Intruder and hopefully something will reveal itself.
I wouldn't stress out too much on jetting and clutching, if it is trying to shift around 7000 RPM....the jetting can be a tad on the rich side and still run well....might be difficult to be on the rich side with the cold temperatures we are experiencing...
Good luck and Happy New Year!