Re: OMC clunk?
Your shift cable it out of adjustment, do as posted above except pull the little cotter pin on you carburetor throttle cable to disconnect it from the carb first, my cobra had the same clunk at idle speed and even though it did it only once maybe twice in a days outing and only just after shifting into gear at idle speed it bothered me, I was able to rectify it by a slight adjustment of the trunion where the lower cable attaches to the upper bracket, while in neutral the trunion should slip comfortably in and out of it's socket, the trunion threads onto the cable and one half turn on the thread is all it takes to be out of synk.
On your Holley idle adjustment there is an idle adjustment screw right where the throttle cable attaches, with the throttle cable still disconnected set the idle RPM, try reattaching the cable and if it fits without pulling on the throttle lever your good to go, if it doesn't you'll have to adjust (lengthen the cable) till it just slips onto the lever comfortably then put the tiny cotter pin back in.
Any farther adjustments on the shift mechanisms get way too involved to even begin to explain, try what we say here, it only takes a very small change to effect your condition, write down and or mark the beginning points of any change you do make just in case you need to get it back where you started.