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OK - terminology issue here. The "shower pan" is a collection liner than underlies the shower floor itself, and is designed (if built and plumbed right) to trap any leakage from the shower floor and route it to the same floor drain pipe. Example image here, copper in this case - 

http://indigochreblog.files.wordpress.com/2012/12/img_0835.jpg

It sounds like your are saying the shower floor or base unit failed - likely a fiberglass or plastic shower, which commonly fail due to incomplete support under them. This can be repaired if fiberglass, but is not usually done unless just microcracking, as it is hard to find an expert - usually you have to have a car body fiberglass specialist or a surfboard repair expert do it, and the color will not match perfectly unless you get a new gelcoat over the entire base unit. Cost about $300-500, ASSUMING the material can be repaired - true fiberglass can, thermoplastic can sometimes be welded but anyone's guess how long it will last without cracking again, plastics like PVC can rarely be fixed so they will hold someone standing on them. Any sort of repair is likely to crack again, because you have done nothing to remove the cause of the cracking which is standing on a base that is not fully supported over its full extent. Some cheepo or desperate plumbers try injecting non-pressuring type expanding foam underneath to improve the support - this does a great job of supporting it but unfortunately supports mold, so starts stinking in short order as a rule.

The normal fix is to remove and replace it, because once it is out there is no sense in putting a damaged one back in for the small increment in cost. Removing it means taking the shower wall liners or the bottom row or two of tile out so you can get the new base unit into place (because they overlap it), then replacing them. So, the $3000 range indicated is indicative of this type of job, which typically runs from a very low of around $1500-2000 for an identical base unit, to more typically $3-5,000 depending on whether a shower enclosure or tile walls. Of course,when the new one is put in, it is CRITICAL that it be fully supported - this means rubbing plumbers rouge or similar marking substance on the bottom, test fitting it, and then lifting it out and checking that all the stiffener ribs and support pads made contact with the pan, and making adjusments as necessary until it has full contact, then standing in it and rocking back and forth to check for any points not making full contat and fixing them.

The $10,000 plus numbers you got must have been for entire shower replacement down to the joists and studs, and the $30,000 range number would be typical for a full bathroom remodel with new shower or shower/tub and doors and surround, wall finishes, vanity, sink, toilet, and flooring and door.

I am not sure a general handyman is the right person for the skylight.  We fix quite a few skylights that were installed by handymen and that could be the problem at its origination.  You will want a roofer for that.

As long as you are splitting the trades at that point, might as well get a flooring contractor to look at the floor once you have figured out the skylight repair/replacement equation.