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Check http://www.sjscycles.co.uk/product-Tektro-Tektro-R556-Dual-Pivot-Caliper-Brake-55-73-mm-Very-Deep-Drop-Nut-Fitting--Front-and-Rear-79.htm

Same way you would leather shoes

Glad to be of help

Check they are tight and the threads are greased

Kneesavers or pedal washers.

Use a genuine Shimano crank tool. I have removed 100's of cranks with these in my career and never failed.

Yes fill the cup with bearings and then take one out.

Long nipples generaly have the same amount of thread, just a blank counterbored end, they simply hide the fact you have few threads in the spoke head.