So, the main factor at play here is turbulence, which is almost never good. Steps and abrupt changes in passage direction create turbulence and turbulence reduces max flow capacity, which limits the efficiency and power of the engine.
I used my dremel to grind down the steps below the valve seats to an even surface. They are visible initially, but as you work on them you will need to use your fingers to feel if there is any unwanted material left
Another area where i discovered a step is where the carb adapter bolts on to the intake side:
Run your finger trough there and you may find that the diameters of the adapter and the passage are slightly different or misaligned. Make a note of where the step is, take the adapter off and grind it down. Be careful not to overdo it, lots of repeated bolting back, checking and taking off will be involved for a proper job.
Finally, there is huge step where the expahust manifold attaches to the head. You can see the difference in the diameters of the seal and the passage here:
THIS IS A DELIBERATE DESIGN FEATURE and you should avoid removing too much of this step. There is a process called scavenging, where the intake valve opens slightly before the exhaust valve closes and some of the intake charge is sucked into the exhaust to ensure the cylinder is completely free of the exhaust gas. This step prevents the exaust from getting back onto the cylinder.
I had to take some of it off to introduce a curve into the exhaust path, and also due to the reason that i have a 225cc, but you should try to keep at least some of this step: