You don't have to bond the conduit if it's only there to "provide support or protection of cable assemblies from physical damage", according to 250.86 ex. 2.

National Electrical Code 2014

Chapter 2 Wiring and Protection

Article 250 Grounding and Bonding

250.86 Other Conductor Enclosures and Raceways. Except as permitted by 250.112(I), metal enclosures and raceways for other than service conductors shall be connected to the equipment grounding conductor.

Exception No. 2: Short sections of metal enclosures or raceways used to provide support or protection of cable assemblies from physical damage shall not be required to be connected to the equipment grounding conductor.

In turn here:

• For your case b), conduit is not required -- NM is routinely run through bored holes in structural members without conduit.
• For d), again, conduit is not required -- you can get away without guards if you run the cable along the side of the joist and at least 1.25" away from its edges. (320.23(B) and 300.4(D))
• As to your protective runs in c) and e) -- 3/4" Schedule 80 PVC conduit has 138mm^2 of usable room in it for a single cable or conductor, and a 6/2 W/G NM-B cable, according to your specs, takes up only 70mm^2, so you have ample space. This might be a tight pull, though, so you may wish to go with 1" instead.
• There are two other things you need to address with your conduit runs:
  1. The conduit you linked is Schedule 40, which isn't sturdy enough to protect wires from physical damage -- the code requires the thicker, sturdier Schedule 80 instead.
  2. Make sure to put expansion fittings in your PVC runs lest they do the snake on you mid-summer, or pull apart mid-winter! Easy rule of thumb for conduit that is operating within oh, 24degC of room temp -- put them in every 4m/12'. (You might be able to get away without it for isolated runs like yours provided the supports are set up so they don't provide excessive longitudinal restraint to the conduit.)