I'm going to install my 3.55 gears this weekend, What to look out for?

Oh boy, are you in for a treat. Just take it to a pro. HONEST. I do them for a living, you need a pinion depth gauge (cheap one is 100 beans). You need a dial indicator and a micrometer or calipers. Also an assortment of pinion shims and carrier shims is nice to have. Every rear housing, and gear set is differant. EVERY ONE. Do a search on the net for rear end set up steps and tech articles, if you are bound and determined to do it yourself. You know, the saying, measure twice, cut once? It appies to rear ends too. My .02
 
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gearheadboy is right - unless you're working with someone that has the right tools/parts and has done it before, setting up a rear end is not something to try on your own the first time, unless you want to pay someone anyway to do it again later.
 
From my experience (engineer for axle manufacturer), Pinion depth gage is a must. Once you get it shimmed right you can start turning the pinion nut down with an impact. The bad thing is you can't just torque it to a certain point and be set. You must tighten a little and then check the rolling torque of the flange and make sure it is within specs. If you overshoot then you gotta start over. Crush sleeves and pinion nuts cannot be reused. Setting backlash is easy. Shim it on the side of the diff gears for propper preload of the bearings. I don't know how Ford does this, some have a shim on each side, some have 1 shim and 1 adjuster nut and some haave two adjuster nuts. Once the backlash is set then use gear marking compound to see how the pattern looks. Some reshimming might be in order. To tell you the truth. I'd have someone who does this a lot build it for you. I've seen axles built a little off and blow up on a dyno. Not pretty. Good luck though.