I'd go 3/8".

If you're looking at increased power now or in the future its nice to have a 3/8' line.  I would upgrade if you're replacing it anyway. 

I am planning to do more upgrades in the near future. Bore and stroke my 289. Or swap it out and go with a 351 Windsor. Do you know about how much 3/8" line id need.  I can buy by the foot so I was thinking 12 feet should do it. For a small piece from the carb to the fuel pump. And from the tank to the fuel pump.

My general rule of thumb for stuff like this is measure front to back and add 5'. 

I wouldn't consider boring and stroking a 289.  I'd thought about doing that to mine at one point, but research led me to conclude that the 289s, because they used such a short stroke, typically don't have cylinders that extend as far as the 5.0 blocks do.  This means that on the downstroke the piston is less stable, which can cause scuffing, friction, and rapid ring and bore wear.  For a lot of other reasons a 5.0 is a much better starting point for a stroker.  But, if you don't already have a 5.0 I think I'd just look for a 351.  More cubes that a 347 and nothing to clearance, stroker kit to buy, etc.