I would run about a 2.25" exhaust all the way if it is a stock to mildly modified 350. If both sides of the exhaust are equal in length, I don't think it matters where you put the H-pipe. The most convenient place would probably be near the transmission tail housing, where it can be its shortest and the driveshaft isn't a concern. The most common H-pipe (I've seen) is the same diameter as the rest of the system.
Also, if cost is a big issue, you could definitely save some with a single 3". While it wont have quite the same sound, a single 3" will support plently of power (confirmed 400 NA rwhp on a late model Camaro) and most likely boost low-end torque. Just make sure the Y-pipe is nice and smooth.
And if you are saying you want to keep as much of the current 2" system. I would reduce it immediately after the headers (as gradually as possible), put a 2" h-pipe near the tail housing, and then simply run 2" straight-through style mufflers. This system would probably be fine if your engine's peak hp comes in before 5000 rpm.