stay away from brake cleaners,
I would doubt if CLR would have any bad residual effects, (most likely it is just a weak acid)
weld in open air and with ventilation, even welding galvanized may get you feeling a bit funny, but there is not any long term effects, if concerned were a respirator,
there are what they call fume extractors basically a vacuum hose that exhaust the majority of the smoke and fumes away from your area,
wire brush the metal or grind it if bad and weld, unless your trying to prepare it for paint or some other reason, I don't think chemical "prepping" is going to do the normal home shop any good,
I did use some steel off a 40 year old irrigation machine, that had a lot of lime and calcium build up on it I just ground off the scale and welded, If I would have been painting I may have used hydrochloric acid or some thing to remove the lime build up, but for welding not needed,
Personally I think,people have been so conditioned that there scared of every thing, today,
every thing has a sticker on it that says according to the state of california if you look at this device you will die of cancer in 24 hours, (or is that it contains materials that could cause cancer) I get confused,
they have people thinking if they see lead paint there going to shrivel up and die,
the same with abestious, and so on,
but many of these same people who have such fears smoke cigarettes, and such,
yes it is good to protect your self, but I doubt if the average DIY is going to suffer any Ill harm from welding on a few pieces of steel,