I want to make a 2-part mould roughly covering 3.5sqmtrs but the overall cost is quite large.

Would it be possible to use a cheaper alternative to the Uni-mould Tooling resin (which appears to be the most expensive part) such as a cheap Polyester resin to bond all the layers of chopped strand mat? Or is there another cheaper alternative to the uni-mould system that would give adequate results?

I don't intend on pulling hundreds of releases, at most I would say 5 in total?

I totally agree that thermal shrinkage could cause even more problems than chemical shrinkage.

But I disagree that we are talking about inaccuracies in a range if thousands of a millimetre. The chemical shrinkage is about a few percent, and the fibre reinforcement reduces that further. But the linear shrinkage is not the main problem. The problem is that this small shrinkage could result in a warped surface, or - even worse - in a twist of your part. This could be very significant if you are producing an unclosed structure (like car hood). In this case the deflection could be several centimetres.
But I case of a canoe you could eliminate the twist during the bonding process, forming a closed structure, wich is much more resistant to torque.