Any bottom bracket can go with any wheelset, so you don't need to worry about that.
The chainline doesn't have to be perfect, but it should be within a few mms of parallel with the frame. I hear it's less of a big deal if you use a 3/32 chain/chainring/cog than if you use a 1/8 setup.
You have that conversion kit; don't worry about others; it's a sunk cost.
Read up on making conversions here:
http://www.sheldonbrown.com/fixed.html
Don't listen to the haters on here that will inevitably tell you that it's not worth it to convert that bike and to instead buy a Kilo TT; you'll learn a ton and love the bike way more if you do it yourself.
Have fun!