I'm no expert but here are my opinions:
1 - a) You can likely continue to drive it for quite awhile but you may be costing yourself more in repairs. b) Yes, try to match RPM, shift smoothly and not under significant load. This will reduce the wear.
2 - a)& b) Can't recall the figures but if you call TH he can give you an idea and point you in the right direction for shipping and what to put the tranny into.
3 - While the tranny is out you should do all you can squeeze into your budget. It will never be less expensive because the major expense (usually) is pulling the tranny and putting it back in.
My understanding, from others that know these vehicles well is that an SVT clutch is quite adequite for most lightly to moderately modded 2.5L's. The flywheel is nice, you do notice the lighter weight.
You don't need an LSD, it's really a matter of what you want. A Quaife or Torsen will help any FWD get its power down. People have said that they put one in prior to doing upgrades in anticipation of needing it later and they were amazed at how much difference it made to a stocker.
4 - Depends on what you endup deciding to do, but there may not be much difference. TH will likely have most of what you need right away. Another shop may need to order parts. Either way you've got shipping time involved. 1-3 days shipping and 1-3 days tranny work if there isn't a wait list.
BTW, don't forget to do the Focus shift tower upgrade while you're at it.
Regards, Alan