At this point you should be looking for any ‘lost motion’ in the clutch release system. While someone cycles the clutch pedal, look at the pedal arm, the upper pivot, and the pedal hanger/mount bracket. is any of this moving. Also check the push rod adjustment to make sure that it is not adjusted too short. You don’t want to be covering the compensation port in the master cylinder yet the primary cup should be right there. Also check that the master cylinder during this cycling to see if it is moving forward with each pedal thrust. I have experienced and heard of problems in the pedal hanger and fire wall causing effective, short stroke. Also have your assistant pull up on the pedal and step on the brake pedal hard and see if there is any motion of the pdeal arm and/or the pedal hanger. In addition look at the carpet and floor mat to make sure that is not limiting pedal travel. In fact, remove the floor mat and pull the carpet back to give the pedal the maximum stroke and see if the dragging clutch problem goes away with a little more stroke.
If you have the specifications for the clutch pedal travel, measure the distance with the pedal up; the distance at the start of feel; and the length of pedal stroke. You might measure the master cylinder stroke but I have not seen any spec for that.
If all is okey here, figure a way to block the slave cylinder so it cannot move the throw our arm. Now feel how firm the pedal is. This should help demonstrate a bleeding problem. If you cannot get a firm pedal here, pinch off the flex line and see if you can get a firm pedal from the pedal thru the master cylinder i.e. isolate the slave cylinder, throw out arm, throw out bearing, pressure plate, and clutch disc.
If everything checks out at this point, try to find out how bad the clutch disc drag is. Raise one wheel (safely). Put the transmission in 3rd or 4th, engine not running. While someone holds the clutch pedal down, try turning the raised wheel. If there is substantial resistance, try mechanically pushing the release arm further and see if the resistance abates.
If all else fails, you will have to go back into the mechanical clutch and recheck everything. Check the flywheel and the disc for axial runout. Check the condition of the input splines i.e. smooth and lightly greased. Check the hub on the splines looking for any catching. Check the pilot bearing for clearance to the input shaft nose and state of lube. Maybe even change the pilot bearing. With the clutch assembled check the uniformity of the clutch release finger height.
Also, make sure you are running the correct oil in the transmission. Some transmission synchros will not allow synchronization with the wrong oil yet still block the shift unless you really push hard.
Hope this helps. Keep posting your progress and the solution you find – we are curious.