I don't think that the treeman's chipper can do a good job for you. It is just not made for that. The properties of the material to be shredded plays an essential part in the conception of a machine.
The limbs and logs hold themselves in front of the knifes, allowing the small bits to be cut off. When the piece of wood becomes too short or too thin, nothing hold it anymore and it is directly shallowed. Not necessarily in a pretty shape, but still, it goes throw. Some shredders have a screen between the rotor and the exhaust chute to limit that.
If the big or long chunks found their way through the chipper the first time, there is a great chance that a good bunch of them will do it again the second time.
Beside of that, the small bits already cut to size will go through too, barely untouched (good thing for your project), but by an enormous quantity at the same time, so the expeller system is overflowed and the chute is clogged (often, it's just an fan-like system on our machines, sending an air flow to push out the chips).
Even if you can adjust optimally the flow rate of the raw chips at the entrance, in fact you will spend a big amount of fuel for too small of a gain at the end.
I agree with MrMoon5shine, first I'd pass the chips pile by a screener to sort out the "good" chips. I think that would be the most cost effective, due to the high percentage of material usable as is. Then, you can find what to do with the refusal : regrind (but it's even more hard to find an economical solution), rot, burn, horse litter (maybe)...
An other advantage of the screener, it allows you to not be too worried with the foreign materials in the chips, contrary to the delicate edges of the chipper