Linear Alternater help

I'm looking for advice from someone with expertise in electrical motors/generators. I am looking to make a linear generator. My question is whether it would be better to use the normal coils wrapped around a tube and edge on magnets (think the shake flashlight http://www.forevershakeflashlights.com/technology.html) or put coils like you would find in an axial coil generator (look down the page http://www.otherpower.com/steamengine.shtml) on a straight base instead of the normal circular one. If it is the shake flashlight configuration I assume it would use axially magnetized magnets (see http://www.kjmagnetics.com/magdir.asp) however I would not know how to space the coils relative to the thickness of the magnet. Would it be based on the length of the magnet or 1/2 its length (ie the length of 1 pole). I understand the axial coil build but not the shake flashlight coil build. The primary build criteria would be energy density per unit length assuming wire gauge and magnet strengths are the same. Yes # of coils and magnets will differ but energy density not how much material's used is the primary design consideration. I can of course experiment but am hoping to wisely use knowledge other have,

Rotary is far easier to control -- you don't need to swap your power generation by direction of travel which is really a pain.
The spacing of the magnets is fairly forgiving, you just need the fields to overlap fairly well, and the field strength is more important than the magnet size. Line up the magnets so the coil passes them N-S and then S-N. Make the coil sides pretty close to the magnet pitch, maybe a little bigger so you are centered on N-N on one side while also centered on S-S on the other side.
If you haven't worked with strong magnets before - BE VERY CAREFUL! They fly together when close and will happily smash your finger in the middle too...make sure you have some wood or plastic standoffs for assembly, and REALLY be sure they are held in place well (best with brackets and screws..)
If your local computer recycler has a pile of hard drives, you can get some nice compact magnets that will work and have brackets installed already: look for a particular make and similar era - the older the better! Getting 2 magnets each from 10-20 hard drives should get you started...

Rotary may be easier but is less easy to seal hermetically in a diy situation. This project is for an ORC low heat, relative to commercial power generators, diy generator that can use easily collected solar (non-concentrated), biomass (wood stove/RMH), waste oil etc as the heat source. Unfortunately the current hermetically sealed refridgeration units are not readily disassembled for conversion to generators. A tube with pistons at each end is easily sealed in DIY. Thanks for the warning regarding rare earth magnets but I've built a few axial flux units and have a HEALTHY respect for their power! Haven't been pinched yet. Your statements seem to imply the shake flashlight configuration may be best. More easily built, yes, but is it more power dense since the magnets are only on 1 side of the coils not both. You talk about "swapping power generation by direction", since I was going to rectify to DC for battery charging could you indicate how that would be affected in a bit more detail, ie what would be different compared to the axial generators I have built. As I said I am not an expert in electricity but do have some hands on experience.

I think the sealing is pretty easy for rotary as well - in a simple sense, you have a barrier with a ring of magnets on one side and the corresponding ring of coils on the other.

Rectifying can help with AC inputs, but you're talking about a low frequency DC signal which will be difficult to work with unless you add real pole switching (with logic or brushes..)