Machining

How much should I expect to pay for the machining for a properly built 4.6 stroker motor?

depends what you want done. Most places charge per cylinder for boring. You're probably going to want them to do freeze plugs and cam bearings while they've got it. I'd also have the block hot tanked, just so it's nice and clean.
I've been looking into it for my own stroker build, and all of the above is going about $250. That's .30 over, new freeze plugs, new cam bearings.

Here is a price list for a shop in WA. I do not know anything about them, just googled and found, but it should give you an idea.

http://www.budsmachine.com/pdf/budspricesheet_0105.pdf

boring cylinders, bearings, and assembly of the block cost me 450, traded out 300 of that. I put the rest of it together ie: bolt on head, oil pump, pan stuff on front....... didn't have any head work done, went with the aluminum head

I called a local guy and here are his prices
Magnaflux $40
Hot Tank $30
Boring and Honing $130
These prices seem WAY better than what everyone payed that have posted. The boring ang honing price is for a small block V-8.

what about freeze plugs and cam bearings?
Do you have the tools to do your own cam bearings?
Freeze plugs can be done with a socket, but it's a PITA. You're at $200, cam bearings and freeze plugs add about another $50, so you're right at what I was quoted.
You can't reuse your old cam bearings if you have the block hot tanked. Here's a link to a homemade installer if you really want to save that $20.
http://www.aptfast.com/Flyer_HowTo_Dir/HowTo_Folder/Cam_Bearing_Install/Install_Cambearings.htm