Actually there is kind of a way which bypasses my lack of knowledge about solving the above (which I'm learning about at the moment actually), as you can prove with vector calculus that the electrostatic potential energy of two particles is q1*q2/(4*pi*epsilon0*r).
The particles will have maximum velocity when all of this has been converted to KE (at a separation of infinity), so equate the sum of their final kinetic energies to the above quantity, and then you can use the conservation of momentum (which sums to 0 here), sub that in to eliminate the other velocity, and hence get the final velocity of one of the particles.
My final result is v1 = sqrt(q1*q2*m2 / (2*pi*epsilon0*r*m1*(m1+m2))).
And obviously the symmetrical result for v2. 
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