With my 15T front sprocket I get a good indication from the rev counter. In 6th gear, 4000rpm = 40 mph. etc 6000rpm = 60 mph. Actually it's a mile or two more but close enough to show me I'm in 6th.
I usually don’t get a “clunk” until shifting into firstNo damage. That clunking is normal. If the rear end doesn't feel like it's locking-up and sliding the rear wheel, you're matching engine speed and down-shifts properly enough. As the bike gets more miles on it, and, as you get more familiar with your shift points and engine speed, it will shift easier and smoother. I'm not throwing stones here.... every bike is different... no matter how experienced a rider you are.. they're all different.. So, all's good.