Couple things:

There is no reason to shift down to 1st at 60+ km/h. At normal street riding this means you would be in third gear. Perhaps second if you like to be higher in the revs.
There is no shifting down in an emergency stop (unless we are talking about a faster stop than normal e.g. light is amber and you won't make it. In that case I'll blip and be in first by the time I have stopped), all you do is pull the clutch in and brake hard but controlled.
Are you perhaps putting slightly more pressure on the (front brake) lever when blipping/braking at the same time. You might also be locking up your rear tire on the hard downshifts. Since there is some play in the chain you might feel a knocking or bumping sensation when it does lock up and skip ever so slightly.

If I come to a corner and there is no real need for braking, I'll blip and downshift, feather the clutch and make sure that I'm smooth. Depending on the corner I might do this for one or two downshifts and rely on a little engine braking. However, when I do this I'm low in the revs. If I come fast to a corner and I blib down whilst higher in the revs, I'm always using the brakes and only feathering the clutch out when rev matched. Don't rely on heaving engine braking when coming in fast, the back might go on a little trip.

Keep working at it though, you'll get it. Did you take the MSF?

 

Heh Steve in that particular discussion the OP was wondering if his tires were causing the rear to lock when setting up for a turn.

With a little investigating, turns out he was trying to transition from 90 MPH to a 30 MPH turn using downshifting / engine braking only. New tires and a perfect suspension setup wouldn't keep the rubber side down with that technique

 

Kuro, can you help clarify when down shifting ( not the purpose of manage speed ) is it only to be in the correct gear for the next maneuver? For excel when needed? I am practicing a lot lately & very surprise how fast I am able to shed speed with only the front brake. ( of course I practice in safe, control environment) I find myself hard to change my old habit of mine. Next thing I realized that I am using downshifting to control speed again. Then I switch to front brake....I think more practice slowly I'll get to 50/50 first, then work my way up. What ratio would you say front brake Vs engine braking is safe? I use to rely on engine brake like 90%/ 10% front brake. After few weeks practice, I think I am at 60/40?

My problem is when I focus on using my front brake more, I tend to forget to down shift gear to collaborate with speed shedding from front brake. i find myself in higher gear for the speed, then had to down 2 gears later....Its hard to describe my question.

 

ahile,
You just need to slow things down a bit sunshine.
I've just read through this thread for the first time and what's coming over to me is 'Noob trying too hard, riding too fast, thinking wrong!'
You've got yourself a fast bike without the necessary ability or experience to know what to do with it properly.
Just listen to what's been said here (most of it appropriate IMO), slow the **** down for a while and start again from the beginning.
Practice changing gears up and down whilst being in relaxed mode. You don't have to race everywhere you go. Just chill out man!
Practice will make perfect. Trying to go too fast before you can physically and mentally handle it will get you smashed to pieces or at the very least cause undue wear on your drive train.
What really scares me about your opening statement is that you insinuate that you need to perform emergency stops routinely. Let me just put that into perspective for you.
I ride about 20 thousand mils a year. If I have to perform more than one a year I'll consider that I'm doing something wrong. I haven't really slammed on for about three years!
Now, just take it easy, don't think you've got to keep up with everyone else. Let the force be with you Skywalker.
Your clonks and bonks will soon disappear as your technique improves. If you still think you've got a mechanical problem take her into a bike shop for diagnosis. That may cost you no more than a pint for the mechanic.
Sorry if droned on but I can't sleep at night knowing that you may be out there riding so misguidedly. I don't want to see anyone get hurt by their own ignorance/inexperience.
Ride safe eh? Let us know how you get on.

 

No worries I actually never knew ther term nor never had anyone explain it to me like you did. I just knew it was bad when it happened to me and had to muddle my way around it myself

 

These two comments confuse me. If you took the MSF, then you should know that in an emergency stop on the street, it is IMPERATIVE that you downshift to first gear. What happens when you do come to a stop but then need to move quickly because the car behind you isn't going to stop in time? If you are in first gear, no problem. If you are in fourth gear, you are squished.