Server-Crash replication agents failing

HI all, We had an unfortunate situation last week as one of our production server
crashed. It was an old box so we built a newbox with the same configurations.
coming to databases, we had the .mdf and .ldf files I have moved those file into
data folder and attahced the databases. Coming to system databases I have just
attached msdb database. I didnt do anything with master and model as we manually worked
with logins problems. Now we had replication set up on our old server(which is crashed)
we have setup the exact replication here. But the problem is some of the SQL Agent jobs
and the replication agents are failing giving different kind of erros.And they run
succesfully if we run them again.
Do you guys think that this is because we have loaded the msdb as it was on the previous server
with new master and model databases(I don't think this is the problem).
Any suggestion would be highly appreciated.
the error messages for replication agent are.
for logreaderagent:- There is another process for log reader agent already running.
other message is :- Waiting for the backend connection to respond.
I hope I am able to explain my situation clearly.
Thanks in Advance.

some other guy did it by running the scripts. I am able to run the agent but it creats million of locks and the other processes fails because of this.
Thank You.