you could cut open the side intake plastic to put air into the boot, and then put heatsinks on the ECU.

Actually it's not on the dyno. My car was dyno tuned in about March last year and had no issues. The problem has only started happening this summer when the weather is really hot. The intercooler barrel in the boot would be hotter too for the same reason, and that is close to the ECU.

ohh. i have a wolf v500 and sometimes my car would do funny things and i ask my mechanic time and time again to find something wrong they never do. its not so bad now, but before on my gt28rs sometimes would what felt like ignition cut of some sort.

I don't have first hand flex fuel experience on the SW20 though I had planed on running it.  The issue with injectors in the 1200+ range is most of them, quite frankly, suck.  I bought ID2000's for my E85 build.  Probably bigger then you'd require for your aspirations however they are a far better performing injector then things such as the 1600CC bosch injectors of old.  Fuel pump is a serious issue.  Not only are you going to need ~30% more fuel straight off the bat due to E85 but I would dare suggest you'll end up be tempted into making a bit more power as E85 will safely allow it.  This means more fuel again.  This leads to a can of worms.  Basically you'll have to run a multiple intank pump setup (couple of stealth 340's or whatever they are perhaps?  If they are E85 compatible) or run a large external single pump.  My general experience with external pumps wasn't so great and I personally probably wouldn't buy another aeromotive pump for my car again.  The SX performance external pump I used was better, however, still suffered cavitation issues after lengthy stints on the dyno and I'd say if you intend on driving it for more then an hour or two straight you'd want to install a fuel cooler in the return line.  I was eventually going to use a weldon pump and deadheaded fuel rail to keep heat out of the pump.  The weldon pump isn't a flow through design so doesn't add additional head to the pump through the fuel cooling the electric motor.  The dead headed fuel rail stopped fuel that had been heated by an aluminium fuel rail attached to a hot aluminium head from returning back to the tank and heating the fuel.
 
I found fueling as one of the biggest pain in the arses in my MR2 build.  Getting something that would work reliably just wasn't that easy.  Another alternatively is running a low pressure lift pump to a surge tank in the boot and running an external pump (couple of bosch motorsports or something, if compatible).  This is cool provided you are happy to loose boot real estate.
 

Rob, I think Walbro do a 400lph pump now.  They have just released a E85 compatible version, per http://www.hptautosport.com/store/fuel-system/fuel-pumps/walbro-400-lph-e85-fuel-pump-w-install-kit
 
I don't know too much about the pump so probably best reading up some user reviews first.
 
May fit intank?  I know evo users had to mod up there fuel pump carrier to get it to fit though as its too big.  That in a single pump configuration should be OK for your goals.

Yeah, dynojet numbers no doubt :P

RacerX just told me that my intake manifold is ready to ship, so I need to hurry up and decide about this Flex-Fuel idea.

Make sure its convenient for you to fill up or have the fuel delivered.
Otherwise it will be a massive pain.