As such there is no transport layer protocol already existing in Castalia. So, you have to implement it from scartch. Although the design of castalia majorly supports variaous MAC/Routing protocols, You can implement a transmport layer in Castalia as an application on top of any existing routing protocol (AODV) in Catalia. Just create a new directory at /src/node/application and code your .c, .h and .ned file. You can borrrow ned file from any of the existing application and chagne it accordingly.
In addition to that, you may have to define a .msg file to create an application packet type which will contain your transport layer specific header informations.
Just modify the codes in "fromNetworkLayer" function in .c file, to describe the actions when the transport layer receive the packet . And, "sendToNetworkLayer" when tranport layer decides to send a packet.
In addition to above all, you need to create a traffic gnenerator for CBR or FTP traffic either as separate application or inside the same transport layer application.
Creating a CBR traffic is very staringt forward. just create a time in the transport layer application and send the packet whenever time exipres, after sending the packet again set the timer for same duration.
If you dont have time to do all this then simply use ns2 and modify the existing transport layer. When it comes to higher layer, either of (Castalia or NS2) network simulator is ok.