There are about 140 instances of the same component and setting the axis and inetrsection each seperately will take to much time. There are a number of problems in the model, the component definition dimension and the instance's are not consistenet to mention a few including heigth. These contribute to the auto fold one sees and if the model is corrected you will not run into that problem.
I have no info to determine what caused all the issues but would suggest to the OP; They spend some time watching the videos on the use of the inference engine; use the projection plugin to establish the plane intersections, Thomthom's selection plugin so a batch selection and deletion of the faces can be done, and make sure the intersections are done in the correct edit context of the entities.massivetriangles_SU8_11_11B.skp

have you look at using canapoy connectors/
http://www.tarps.com/fittings2.htm

Attached is correction to your model , or rather the lower surface. Both top and bottom showed the same problem so I assumed fix for one would be good for the other;
1.A new component for #94 ( I called support ) was made to correct some small dimensional inconsistencies;
2. Out-liner was used to select #94's, move them up off the surface and the component browser “replace selected “was used to replace them with the new support;
3.The supports were cut and pasted in place to move them to separate context;
4.The rendering was changed to wireframe and then hidden resulting in a clean window with no geometry;
5. Ctrl+ A was used to select , then delete to remove any extraneous entities in the model Note; this render mode when hidden is not selectable by SU ,so they were unhidden.;
6.A new surface( problems corrected here also) was drawn on the ground plane and a plugin called “smart drop” used to place them back on the surface and an intersection done with no auto fold this time;
7.A left to right selection was done selecting both intersection edges and faces ( don't select the total surface);
8.Thomthom's selection toys was used to deselect the edges allowing all the faces in the intersection to be easily deleted.
You need to change the units you use. A 32 bit float which SU uses has a 7+ bit percision and using 2 place meter does not show thw resoloution you need
Good Luck

massivetriangle_SU8_11_11A.skp

You cannot use the orginal model you posted? I have done a number of dimensional checks and can not find any smoking gun but in some cases the intersections do not happen the way I think it should. Do you need the supports to be hollow? Trying to put top /bottom surface could help?

This tut gives info on the intersections http://sketchucation.com/resources/tutorials/37-beginner/433-the-basics-of-intersection-in-sketchup.
Removing unneeded materials wwould help on reducing model size.Actually the model is realitive simple and should not be ~20MB

Attached is quick look.
Used outliner, selected all the support components, moved them up above surfaces.
Deleted the surfaces you posted and drew new bottom one, moved supports back then drew second surface.
I also removed you materials, did purge and fix problems. For those condiditions model size is ~40kb no auto folds.
When doing intersect some componts intersect with surface others do not even though all the same componets which i do not understand yet?
I have some thoughts why you had the orginal problem most probable is you slightly moved a vertices causing the auto fold but dimensional checks does not confirm that.

massivetriangles-SU8_1.skp

Note the top and bottom surfaces are very different, the top has a number of stray lines(~31),use the text tool to check the location of vertiecs and you see you get the sense the surface is distrorted, change the model units and remove the two place meter and use something that gives more resolution so you can see what is going on ( like 3 placs mm. So now the question is how to correct without a lots of work. luckly the supports are components so you will not have to redraw them.
I have to convert your model to SU8 before i can go further.

Auto folding?:
Can you post yor model?

I could care less about that. If you are comfortable with your " design" spend all the money you want on it.

Can you cite a link to back that claim.
The link I gave you is independent of design but the actual energy content of what is used unless they are BSing. Unless I used the data wrong then that should be the bottom limit
If you are going to spend $ to build the system you want to use the same approach you cited for design and understand first.
I would not rely on what the designer states now until he has proof.
BTW FMEA demo project, somewhat old now, stated 20# wood is equivalent to 1 gal of gasoline.

Interesting, I did not know wood gasification was used in Europe during WW2.
FYI after doing some search and finding https://bioenergy.ornl.gov/papers/misc/energy_conv.html: For the 10KW generator operating 3 months @ 12 hours /day with air dried wood (2% moisture content) about 2.6 tons of wood needed.

usually you can let the program do the calucations for you. However,the drawings you have posted do not make sense to me, some dimensions I have questions plus what is meant by unfolded?
Since you have drawings can you post more info like assembly drawing etc. or the whole pdf
Thanks

There are a number of suggestions here https://sites.google.com/site/sketchupsage/faster.
Many yimes the large size is cause by use of photo textures which are too big.
Try setting you rendering option to monochrome while you model and see if that helps and use textures for " show and tell " etc.
In windows , model inf, stats do a purge to get rid of any unused " stuff"
Post the problem model if ok to do so, the size you have is too large for an upload herein ( 10MB limit), so you will have to use a file sharing site like drop box or Google drive, load there and then post url location here.

And this http://www.stratasys.com/~/media/Main/Secure/White%20Papers/Rebranded/SSYS-WP-AccuracyMyth-03-13.ashx
copy and paste link

FYI; some interesting info https://www.google.com/search?sourceid=navclient&ie=UTF-8&rlz=1T4NDKB_enUS554US555&q=jay+leno+3d+printing

fYi, video of jay Leno and making a part for his 'old" car and 3d printing it.
http://www.youtube.com/watch?v=7ZrJsrTT4EA

FYI: With all materials removed model size is 7.98MB

If you save your materials as a collection you will then have a skm file and can quickly look at file size to home in on the major contributors.
For your case the material 2 skm is 6.544Mb and panca tattva PNG background is 2.324MB. You then have a a few 10-15, I did not count, in the range of .5MB each. So if you get the material usage file size down you maybe able to save close to 10 MB.
The rest of the reduction to get down to your 2MB target will require geometry work. That is difficult to do and I would expect maybe an additional 2mB reduction so you target will be very difficult to meet
I have not checked yet but make sure you have not used a lots of unique components. That step can add up to maybe 30% in file size increase vs two components.
You can make a quick check on what you can save in the material arena. Use one of the plugins and remove all materials.
Good Luck

I upgraded but then when I saw how sloppy Trimble implemented the conversion to free I removed the program in total.
By sloppy I mean they leave all the Layout and StyleMaker code on your machine which are files for the Pro version

When you toggle zoom extents the program will display the total model with some parts you do not realize you made. It could be a very short line you cannot even see.
Suggest you select the model( double click), change the rendering mode to wire frame and hide it. Then do a select all and delete. Un-hide your model and then do the zoom extents again.
Hidden wire frame is not selectable so this will only delete the items you do not want. Save your model first, this works through Su8 I've not check if it is ok for 2013

Not sure what are doing but Su does not use layers for geometry isolation only visibility control. All primitive geometry always goes on layer 0.
Geometry isolation is done by the use of components & groups.
If you have any non components or primitive geometry you are trying to control with the layer manager select those and use the delete ( circle with - in it) and select the option to put geometry back on layer 0.