Here's the problem with just removing one line and capping the other hole (or leaving it open)
If you cap the line port and close the bleed screw, as you apply the brake, it will draw a vacuum on the closed off side and you will have vacuum working against application. If you leave the ports open, dirt and water will enter the piston bore causing it to lock up. To get full operating pressure, you would have to close off one line port and cap the bleed to the smaller of the two chambers and remove the smaller bore piston seal you could use either line port for pressure while capping the other port, but you would have to bleed the caliper from the bleed port on the larger chamber. If I were to do it, I would use the small chamber line port instead of the large chamber port - reason; with the small piston seal removed, pressure would initially push on the smaller surface area first, push past the piston and enter the larger chamber to push on the surface area there providing 100% of available pressure to the brake pad.
Bleeding would be tricky as air would tend to become trapped in the piston seal groove that the seal was removed from. If I were to do it, I would reverse bleed (push the air to the MC for expulsion). Holding the caliper so the piston bore is vertical, I would fill the caliper with brake fluid - with the cap off the foot pedal MC, push the piston in until it just contacts the piston seal and attach a c-clamp to hold things in place (the c-clamp will be used to push the piston all the way in later) - with the c-clamp holding the piston in place just enough to prevent leaking or spillage, move the caliper to the lowest point possible - put enough fluid in the MC reservoir to cover the bottom of the reservoir and wait for any air to escape naturally (if there is any air bubbles coming up into the reservoir, just add enough fluid to keep the bottom of the reservoir covered) - once all the air that wants to escape has, turn the caliper so the line port is at its highest (caliper at about 45 degree angle with the line port at the apex) - use the c-clamp to push the caliper piston into the caliper body (if it is not straight, you may have to re-position the clamp or use water pump pliers to push down on the high side of the piston) - as the piston is pushed slowly into the caliper body, the fluid in the caliper piston chamber will be pushed through the line to the MC reservoir - push slowly so air will be pushed ahead of the fluid - if the reservoir gets too full, sop out excess with a paper or cloth towel. When the piston is fully seated in the caliper & before removing the c-clamp, operate the MC to see if the system pressurizes - you might have to bleed the MC - turn the caliper so the piston is vertical - push on the foot pedal, hold it down, crack the line bolt to let air out, snug the bolt and let off the pedal - repeat a couple of times - if still not getting normal pressure, loosen the c-clamp about 1/2 inch - pump the pedal - the piston should move out about 1/16 inch - when you let off the pedal, the piston may retract about 1/32 inch - wait about 15 seconds between pedal pushes - when the piston is pushing against the c-clamp, hold the pedal down, tip the caliper so the line fitting is at the apex, loosen the line fitting just enough that fluid escapes and tighten - let off the foot pedal and wait about 15 seconds - press the pedal down & crack the banjo line bolt on the MC just enough that some fluid escapes - continue to hold the pedal down & tighten the c-clamp to force fluid and air out of the fitting then tighten the banjo bolt - let off the foot pedal and check operation - if necessary repeat all the steps - when all the air has been purged, pressing the brake pedal should spread the c-clamp about 1/8 to 1/4 inch and when the pressure is relieved the clamp should push the piston back.
Now remove the c clamp, install the brake pads and caliper - make sure the reservoir is filled to the upper line install the reservoir bladder and cap - pump the pedal until the brake is applied and had normal pressure. Hold pressure on the brake and crack the bleed screw just assure all air has been purged - tighten the bleed screw before letting off the pedal.
Not how much fluid is in the reservoir - this is an indication of how much wear there is on the pads - DO NOT TOP OFF THE RESERVOIR - when the brake pads are worn out, the fluid level in the reservoir will be below the lower line - when you install new pads, the fluid level return to normal when the piston is depressed - with new pads installed, the fluid level may be topped off if necessary - do not add fluid between pad changes unless the has been a leak or other problem.
Have fun - this job should keep you busy for several hours and depending on parts are needed and where you have to get them could stretch into a week of occupation.
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