Recently, nano-systems based on molecular communications via diffusion (MCvD) have been implemented in a variety of nanomedical applications, most notably in targeted drug delivery system (TDDS) scenarios. Furthermore, because the MCvD is unreliable and there exists molecular noise and inter symbol interference (ISI), cooperative nano-relays can acquire the reliability for drug delivery to targeted diseased cells, especially if the separation distance between the nano transmitter and nano receiver is increased. In this work, we propose an approach for optimizing the performance of the nano system using cooperative molecular communications with a nano relay scheme, while accounting for blood flow effects in terms of drift velocity. The fractions of the molecular drug that should be allocated to the nano transmitter and nano relay positioning are computed using a collaborative optimization problem solved by the Modified Central Force Optimization (MCFO) algorithm. Unlike the previous work, the probability of bit error is expressed in a closed-form expression. It is used as an objective function to determine the optimal velocity of the drug molecules and the detection threshold at the nano receiver. The simulation results show that the probability of bit error can be dramatically reduced by optimizing the drift velocity, detection threshold, location of the nano-relay in the proposed nano system, and molecular drug budget.