A few comments...
1. Could it be that the problem is caused by a short lever? The shorter the lever, the less leverage you have while squeezing the lever. Try to install a regular length lever. On top of that, try holding the throttle with your thumb and indexed finger while braking with the rest of the fingers (like in OK sign below). This way you are squeezing the lever at the furthest point from the pivot point - thus producing more effort at the master cylinder. This also makes it easy to cover the brake lever all the time.
2. If you use some sort of vacuum method of bleeding the brakes at the caliper, some air gets sucked in throught the bleed screw. It didn't come from the caliper - so I wouldn't conclude you had air in the system solely based on that. When bleeding this way you always see a trace of bubles coming through the clear hose.
3. Prior to a regular vacuum bleeding, you can try to feed the fluid through each caliper using some sort of syringe (I used the one to fill ink cartridges). This way the air gets pushed up and is much less likely to stay in the system. Just make sure you have no air when you connect syringe to the caliper bleed screw via the clear hose. Another words, connect the clear hose to the bleed screw, fill with fluid, have a filled syringe completely filled, stick the syringe into the hose and slowly push. Repeat until you see fluid coming out in the reservoir. When this is done, you can continue with regular vacuum style bleeding for a bit.
4. If the braking system was fine right after you bled it, but after a few days feels spongy, this obvously means you got some air in there. Wipe everything clean around calipers, banjo bolts, lines, master cylinder, reservoir , then queeze the lever and hold it there for a minute while squeezed. If there is even a tiny leak, it should show as a tiny drop. Another silly possibility - you didn't leave the reservoir almost empty, right?
5. Another possibility is that you master cylinder does not seal 100%. However, if this was the issue, you would experience the problem all the time consistently.
6. Another possibilty is that some of your pistons are stuck pretty bad and it takes a lot more effort to get them moving. But again, you would experience the problem all the time regardless of bleeding.
7. Try EBC HH pads. They made a huge difference. You can also try EBC HH Extreme (not sure about exact name) - those are pricey, but even better.
8. Take a look at your brake pads - do you see any silverish spots on them? If so, they are glazed and their braking ability is greatly reduced (remember when you were braking from triple digits almost to a stop -that did it). Rub them against 100 grit sandpaper (i.e. put the sandpaper on the flat surface and move glazed brake pads on them). Once you got rid of the sliverish spots, put the pads back on, and treat them like new (i.e. you have to brake them in gradually).
Report back with your findings. Please try to be very specific - devil is in the details.
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