I just had a new clutch and flywheel installed on my 03 350. However I'm having difficulty getting the car to go into gear (mostly first) it also seems my clutch pedal is pretty soft. Is it likely a leaking master or slave cylinder is the cause of this? Also I had trouble getting the car into gear and a soft clutch before the new clutch/flywheel was installed.

 

Possibly yes, have you checked your fluids?

 

How many miles are on your car? Getting a master, slave, and steel braided clutch line as a combo is the best idea because then you only have to bleed the system once and you'll have perfect pedal feel. I got the cylinders from Rock Auto for super cheap. The master is a little annoying to install, but the slave and clutch line are stupid easy. Bleeding the system when it's bone dry is a bear, but I figured out a fairly easy way with a hand pump from Autozone. That's unless you're just gonna have a shop install them.