Brilliant anyhow Duck, Jargon notwithstanding.
Those wafers whose tabs extend beneath the key (under the straight/flat side/part of the "keyed" section of the key) are not being lifted up high enough due to the cut in the key being too deep. Dremel those ones down (or up actually).
But for the ones that extend up above the key (over the bumps and valleys of the cut part of the key) they are riding over a key cut that is too high. Those wafers may have the aperture inside the key channel cut taller (i.e. deeper), thereby lowering the wafer and its upward extending tab, bringing it down to "shear" (more Jargon for you from another show off Smithy, a shear cylinder is smooth and will turn)
This would increase the "overall degree of security" of the lock in that there would be fewer key combinations that would "unlock" it. The wafers are designed so that one key cut depth holds the wafer centered so that its upper and lower tab are both in shear. If it is raised too high (or not high enough) and the tab is filed down, then you are adding about two more key depth possibilities per millimeter removed. In the bigger picture, who f'ing cares. I think the method you have developed is genuinely genius. But if you would like to take it up a notch you consummate craftsman...
Pull the wafers out of the cylinder straight in the direction that the spring is pushing, and yes the spring is in that alternating round hole at the end of the slots. It should come out like an old 8-track tape cassette with a small "spur" that keeps it seated (pull it in & out 10 times and it will no longer stay in having scraped a furrow in the cylinder), mind that spring by the way (I have not seen but one spring per wafer, just the two pieces). For extra credit, see if there are any wafers that may be traded/switched so that there are fewer that are "too low" (for too low cannot be compensated for, barring wafer replacement). See if you can match the wafers up to the key cuts so that as many as possible are "too high" in the cylinder.
Now take a small file and enlarge the "hole" in the center of the wafer where it rides on the key bumps. Doing so will lower the wafer so that its tab can get right to shear (if you are good enough with the file) OR just get it "close enough", then Dremel it. I suggest working one wafer at a time as you reassemble the cylinder.
Again, not a criticism. Just my $.o2