1) Here we see an overview of the item input side. Saplings and apples are put into those two item tesseracts. (Scrap the third filter with the enderchest, it is completely unnecessary, forgot to delete it.) Should those two tesseracts ever backlog, they will fill the barrels (there is a restriction tube avobe the log-barrel). Logs will rise up in the tube and go throught the top filter into the stacked hoppers, which fill into the TE pulverizer.
2) The pulverizer will produce planks at max speed, using 2 MJ/t in the process. They get auto-ejected into the relay, which feed the tubes leading to the boilers. The (TE-)sawdust is entered into the diamond chest (could be any kind of inventory, cheating stuff in for experiments kinda leads to oversized stuff), autocrafted to compressed sawdust and pumped into the powered furnace (the second gray block next to the RE-Cell), which ejects into the tube network.
The cell is fed by two TE steam engines (second one is below the cell, AqAcc for water can barely be seen beneath the visible steam engine). These are powered from the charcoal. The filter next to the boilers also accepts charcoal. This will be used, when the plank-reservoir will dry up (the sawmill is just a tad to slow to keep all 3 36HP boilers running with planks alone). If neither the steam engines nor the boilers need the charcoal, it will first fill the diamond chest next to the manager in the background and finally, if even that chest is full, fill the barrel in the back. That manager will keep the cargo manager stocked with a stack of charcoal.
The filter 3 right to the steam engine is set to planks. If everything works normally, nothing should ever go through there.
3) Manager 1 is the manager at the charcoal chest, Manager 2 is the manager at the cargo manager (CM). Since my tracks connect to the CM on the red side, the options are set red. You could also remove the saplings from manager 2 and remove the "fill saplings" instruction from the CM without problems.
4) This shows where the tubes, which went underground before the charcoal-filter, come up again. Important here the equidistance between the two inventories.
Hello mister slime!
5) Now over to the liquid side. The front tesseract feeds apples into the squeezer, mulch is pumped out to the left, apple juice to the front into the single BC-tank. The back tesseract feeds saplings into the fermenter. The whole setup is powered via 7 industrial steam engines on one of the liquid boilers. Try out, if 6 engines suffice.
6) Below the tank is gate, set to (IF tank==full THEN emitRedstone). This redstone signal is sent via the (lime green) jacketed wire to the AqAcc below the fermenter. Result: Water will slowly drain from the fermenter. As soon as the liquid tank is empty, apple juice will pour in, which will in turn drain the tank, which will deactivate the redstone signal, so the water will start to refill, as soon as the apple juice has been used up. Mulch is pulled from the ender chest via an autarchic gate set to (IF fuel<25% THEN pulseEnergy).
All six sides of the fermenter are used (apple juice, water, mulch, saplings, energy, biomass out).
The mulch production from the apples is a little bit too low, so another method of mulch production needs to be added. If this problem is solved, the setup produces just enough biofuel to feed 5 36HP boilers.