Ok... there are a few things of note in your comments... ones that are quite easy to remedy, and I have some ideas for the others. 1) Timing of the button presses. If you press it for longer than 5.5 seconds and it's going 'silent', in reality, it's being pressed for 7+ seconds. The 7 second press causes it to "forward" all commands to a second Mk2 unit. It will only cancel that mode with an 8 second press. The solution is to shorten your button presses by 1/2 of a second to ensure you don't go over that limit. The time that the gcode has is the actual time "on the button", but if your unit is triggering the button a little earlier, then the time it takes to press the button and then back away from it can also add to that total time. Shortening that press time will take care of that. Also, make sure you're trigger point is exactly .1 or .2 mm prior to the actual distance you enter into the gcode generator. If it's more than that, remember, it takes 1 second to go over 25mm... which means it can take an additional 125ms for .1 mm of travel... time two = .25 seconds just for .1mm of travel both ways... if your button press is actually .5mm late, than you're adding an additional 5 x .25 = 1.25 seconds to long. (If you simply shorten the time on the button, then you don't have to worry about these calculations... it's the total time that is important... where you subtract it doesn't matter, if that makes sense.)
2) You can't use relays to switch the motors with modern electronics. The Mk1 version of the 3D Chameleon used exactly that method, which fails with modern TMC devices due to their "break detection" circuit which causes the stepper motor drivers to shut down. They won't restart until you recycle the power, which is not an option with these electronics. Also, Creality machines (in particular) and their derivatives, tie all the enable pins on the X, Y and E stepper motor drivers together, so it makes even software resets impossible.
3) Our Mk3 already is design complete and includes the extruder built in. (Similar to the current model where it's actually installed in the extruder replacement scenario.) If you'd like, we can send you the replacement plastic parts to make your Mk2 an Mk3 (or, technically, what we're calling the Mk2+) which should give you a much stronger drive. (It's has about 3x the grip on the filament of the old design... and is tunable.)
4) The inconsistent drive... with the Mk3, we improved the grip strength by about 3x over the Mk2, which should easily over power any friction points in the PTFE or the Y adapter. Mind you, the Y adapter is 1.85mm ID on the inside... so if your filament is larger than that, it will get stuck there. Relaxing the compression on the Y adapter by 1/2 turn is the correct path there... however, if you're using Capricorn tube in the hot end, be aware that Cap tubes are 1.95 ID +- .05... so you mileage may vary on if it'll fit or not. Our 1.8mm ID tube in the hot end should constrict it to smaller than the Y adapter. Cap tubes above the Y adapter should be just fine as well as between the Y adapter and the extruder.
5) Tip shaping... with the Mk3 parts, the drive system should be significantly stronger so the tip shaping is much less of a concern. Stringing is the only real concern. With a smaller 1.8mm ID tube in the hot end, and the stronger grip on the filament, you should see far fewer issues like these.
Bill