removing protective comonents is NOT RECOMMENDED. Use of a cable without the clamping diodes might lead to damage of the DVI encoder chip. Your cable is not complete without the clamping diodes.
Your video title is misleading. What you see is a Blitter glitch, not an Indivision AGA MK2 glitch. Just like the old version of Indivision AGA, this new one takes the AGA chipset to it's limits, and on some, you see that timing errors of the chipset have not been corrected properly on all boards. If you remove Indivision AGA MK2 and display that video mode on a monitor that can handle these frequencies, you will see that the glitches are still there.
You may have to do more tweaks to your mainboard. This looks like a wrong blitter call, where your accelerator's timing does not match the mainboard's timing. I'm assuming that this is the cause for the Blitter doing funny things in your computer.
Your photo shows two arrows and "0.5k" - if that means that the resistance between these spots is 0.5k, then the falling edge of the CCK signal gets too flat, probably making matters worse. Check E127R (might have to be replaced with a ferrite) and E127C (might have to be removed), but also the usual suspects E123C and E125C that may have to be removed for proper accelerator operation.