Connections in load flow analysis
Load flow analysis usually deals with systems with nodes which are connected by more than one line.  An admittance matrix describes the connections between the nodes.  You can see more about the admittance matrix here:
http://en.wikipedia.org/wiki/Nodal_admittance_matrix

The different line lengths are taken into account in the admittance matrix.  The longer the line, the higher the impedance, and the lower the admittance. If there are no controllable components in the system, you cannot take current limits into account, since the currents cannot be steered.

You do not need to divide the nodes between generation and load nodes.  For each node you need to know either the active power and voltage (PV node) or the active and reactive power (PQ node).  You can sum the impact of the generator and the load.  Often, if the node has a generator, then it is a PV node.

The reactance of transformers is very high compared to the reactance of the lines themselves, and thus cannot be ignored.  A transformer can be represented by an impedance, which can be added to the impedance of the line to which it is connected.

I'm not sure what you mean in your last question, but if you are asking if the system needs to be simplified so that it is represented as a chain of nodes, then the answer is no.  The admittance matrix describes the relationship between the nodes, and can accommodate systems more complex than a chain.

If your system has 300 nodes, then your system is fairly large.  For systems larger than a few nodes, calculating an admittance matrix by hand is laborious.  I would recommend using power flow software to perform your load flow.  A fairly comprehensive list of software for power systems analysis can be found here:
http://www.openelectrical.org/wiki/index.php?title=Power_Systems_Analysis_Software