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I've found the only way to align stubborn calipers is to eyeball the rotor /pad gap and then tighten bolts slowly and evenly.

What exactly does the hayes tool accomplish other than initially increasing the rotor pads gap?
The Hayes tool (and other brand shim tools) lines everything up before you cinch the bolts down down. You insert the shims, squeeze the lever, then tighten the bolts. Any pad gap will close up after a couple of squeezes.
 
I had this issue before on some brakes. In most cases it is a bolt that is not true or has some head wear, or washers that are worn out, and have uneven surface. This will cause the caliper to move when you turn the bolts.

Another thing can be wear at surface where the caliper and adapter/frame touch each other (on either the adapter or caliper). Sometimes you can see gouges, and the caliper will want to "fall into place" into that position when you tighten, usually from previous over torquing.
 
I use a gap tool made for setting valve/lifter gap in engines. You can buy them at any parts store for less than 20 bucks. Get the ones that are for setting valves and not spark plugs. Experiment a bit with what shim you want to use but I usually start with the .009" and slide it in on the side that is rubbing (between the rotor and pad), then loosen the bolts, put on brake pressure and re-tighten. This is a quick and easy way to get about 75% of them lined up. If they still drag (Magura's are the worst I've owned because they barely retract) then use a light and try to see which way they are cocked. Try just loosening one bolt and leave the other semi-tight and go again. You need really straight rotors with Maguras.
 
I use a gap tool made for setting valve/lifter gap in engines. You can buy them at any parts store for less than 20 bucks. Get the ones that are for setting valves and not spark plugs. Experiment a bit with what shim you want to use but I usually start with the .009" and slide it in on the side that is rubbing (between the rotor and pad), then loosen the bolts, put on brake pressure and re-tighten. This is a quick and easy way to get about 75% of them lined up. If they still drag (Magura's are the worst I've owned because they barely retract) then use a light and try to see which way they are cocked. Try just loosening one bolt and leave the other semi-tight and go again. You need really straight rotors with Maguras.
Not a bad solution but they make the tool specifically for bike brakes and they're under $6

 
Not a bad solution but they make the tool specifically for bike brakes and they're under $6

Do those work well?
 
Interesting all of these folks that struggle with centering a caliper. I know some are more challenging than others, but in 20+ years, this method works every time and usually easily for me. Perhaps it's an acquired taste.
I wouldn’t say I ever struggled with it per se but the Hayes Tool makes it a zero effort, don’t even need to try job. If I never had one I’d be just as successful but I would have spent far more time doing so.
 
I'm having a consistent issue with my Magura brake calipers that they always end-off misaligned with the rotors slightly.

With the bolts just slightly loose (so that the caliper is free to move side-to-side but not wobble too-much), I hold down the brake lever to center the calipers on the rotors, then tighten the bolts. I go lightly at first, and alternately between the top and bottom bolts until they are tight to feel (I'm not using a torque wrench).

EVERY time the brake pads end-up nearly rubbing on one side of rotor and with a noticeable gap on the other side, though they are parallel to the rotors. Doing the process slowly, its clear the turning of the screws moves the caliper inboard.

Does anyone know how to avoid this issue? Should I put a shim in there to prevent this while tightening down? Or is there something wrong with my bolt or how I'm tightening it? Am I over torquing and that's causing the movement?
The brake mounts need facing.
 
I have one of the oval alignment tools as shown in the picture. It has really grown on me as I get better positioning and usually pretty close to equal caliper piston movement. At first I forgot I had one. A buddy gave it to me. I tried it when I could not get good alignment with the lever squeeze method after too many attempts. I use it every time now when I align calibers (brake bleed, new pads, new rotor, etc. ). First attempt I do not even squeeze the lever which usually works especially for new pads. If still a monkey hair off, I may squeeze the lever two monkey hairs(one for each side). Don't forget to take it out when done !!! :D

Image
 
I'm having a consistent issue with my Magura brake calipers that they always end-off misaligned with the rotors slightly.

With the bolts just slightly loose (so that the caliper is free to move side-to-side but not wobble too-much), I hold down the brake lever to center the calipers on the rotors, then tighten the bolts. I go lightly at first, and alternately between the top and bottom bolts until they are tight to feel (I'm not using a torque wrench).

EVERY time the brake pads end-up nearly rubbing on one side of rotor and with a noticeable gap on the other side, though they are parallel to the rotors. Doing the process slowly, its clear the turning of the screws moves the caliper inboard.

Does anyone know how to avoid this issue? Should I put a shim in there to prevent this while tightening down? Or is there something wrong with my bolt or how I'm tightening it? Am I over torquing and that's causing the movement?
I have had good results with the method you are using, but you do need to compensate for the bolt tightening induced caliper movement by starting the caliper slightly offset the other wayso that once you have nipped up the bolts the caliper is perfectly centred.

There might be a technical reason for this issue like others have suggested, but I just do the above and go ride.
 
It’s a slotted bolted connection; as it’s tightened, the rotation of the screw head (and possibly the threaded shaft as well) will tend to favor one side or the other and produce a pushing force along the slot. (Also the “worn groove” and “keyed into place” factors as well. Add a thin washer to mitigate all that.
 
To make it easy to see the disc contrasted against the pads, I use a big piece of white paper or a towel under the bike. Even better to do it in bright light.

Sometimes it's easier to do the aligning on with the bike in a workstand, sometime upside down.
 
Had a similar problem on an old frame.
Thought that this is the reason some brakes had concave washers there so the calipers could be slightly adjusted. Bought a few, put them in, never had problems anymore.
idk if thats the right applications and I am no bike wrench lol.
These turned concave on my setup
Sure that this is not by design?
 
99% of the time when calipers are aligned at low bolt torque and out of alignment at high bolt torque, the frame is not properly faced. Many times the fix is as simple as scraping a bit of paint off of a brake mount post with a razor. Other times re-facing is required with a proper cutting tool. Be reeeeaaallly cautious and triple check the current post height and bolt hole depth before cutting away frame material. On rare occasions, the frame has been over-faced at the factory (or by a previous mechanic) and further cutting of the post will either make bolt depth too short for safe clamping or require shimming to bring the caliper height back up to match rotor placement.
 
I'm having a consistent issue with my Magura brake calipers that they always end-off misaligned with the rotors slightly.

With the bolts just slightly loose (so that the caliper is free to move side-to-side but not wobble too-much), I hold down the brake lever to center the calipers on the rotors, then tighten the bolts. I go lightly at first, and alternately between the top and bottom bolts until they are tight to feel (I'm not using a torque wrench).

EVERY time the brake pads end-up nearly rubbing on one side of rotor and with a noticeable gap on the other side, though they are parallel to the rotors. Doing the process slowly, its clear the turning of the screws moves the caliper inboard.

Does anyone know how to avoid this issue? Should I put a shim in there to prevent this while tightening down? Or is there something wrong with my bolt or how I'm tightening it? Am I over torquing and that's causing the movement?
It's simply that the bolt heads are moving the caliper during that last bit of tightening. Try placing a washer between the bolts and the caliper. And eyeball the position of the caliper when squeezing the lever, and manually readjust (holding onto the caliper also) after initial tightening.
I use those dome washers off V-brake pads for this, along with slightly longer bolts to make up for the height difference.
 
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