Let me get this straight (I think you might have been in a bit of a rush, but you don't seem to be a bot):
You replaced the engine when you got the car because the bottom-end had gone on the old one.
You also had the turbo recon'd (so it was rebuilt within the last 3 years).
There's an AFC and tubo timer working, and a boost controller than you think isn't working. - However, you may have messed-up the settings on the AFC by playing with them?
The pipe that goes to your (stock) boost guage sender has split? - You can just cut the split bit off and block it off, but you will have boost problems if you just leave it.
You're having problems driving it when it ties to come on boost? - That'd be the split boost pipe; it doesn't take much to upset it.
I don't know about the white smoke either, but when I had a boost leak I didn't keep trying to push it so I'd guess it's to do with the fuelling (rather than a blown head gasket which would be water vapour). - I'd get that hose blocked or replaced and see how you go. You might want to clean the plugs as they've probably fouled (which won't help anything).
You'll want to get your fuelling looked at if you've messed-up the AFC settings... I'd suggest a rolling road for that so that you can monitor the air/fuel ratio.
Get back to us, and let us know how you got on. - How about introducing yourself and your car?
EDIT: There's a move to delete the posts of people who join-up and don't introduce themselves, but it's not a rule yet so I'm letting it go.