I had the "clunk" on my 1997 in about 2003 or 2004. Noticed it packed heavy, two up going to NH for the week. Chased my tail for a week or two, turned out the motor mounts where shot. I changed both with new form the MoCo and she has been fine since. But yeh, you need to change front and rear. How it happened is up to debate. My unproven opinion was that after some service I had the bike running on my Harbor Freight lift, no fancy frame spacer. So the lift was holding the frame and the transmission at the same time, with the motor running the force on the non-moving motor got transferred to the motor mount, and you get the "clunk". This is an unproven theory, but I never started the bike again on the lift, and I never changed the motor mounts again. Good luck.

 

Thanks Architect, my first thought it to get the back raised and put the pressure on the front end and try and recreate it like I did the last time when i thought it was just the front motor mount - and then listen and search to see where it might be coming from.
I hope it is either the rear mount or the front head bolt which i've also heard makes this sound.
I've just spent a lot of time on this bike "fixing" things to then find it it wasn't broken and now something else is acting up, so want to be at least 80% sure before gong down another rabbit hole!
Thanks!

 

""Unfortunately it has not fixed the loud "clunking" noise that i was getting while running, especially at around 2000rpm like something was loose and hitting the frame, for example the transmission clunking when i go over a bump.""

Have you checked the tension in your primary chain?

 

Thanks Jake, yes i opened the primary and checked all around inside and all appeared correct.
I have just received my rear motor mount and once i change it today ill see if that was the "simple" problem. I will come back and report.

 

GREAT NEWS!
Well gents, the good news is that it was the rear motor mount. It was shot. After putting it on yesterday I went for a trepidatious ride but she was riding sweet!
The learning for me was that it definitely sounded like a loud clunk...it felt like it was coming from the front for sure, it was difficult to replicate on a stand so hard to locate and it was a lot worse with a passenger which is how it started and should have given me a clue. So gents, quite a boring post but thanks for the support and ideas!

 

AWESOME...!!!!!
Congratulations, and thanks for reporting back.