Is the noise coming from the bellhousing area or the trans itself or can you not tell? I'm going to guess if it goes into every gear ok without grinding its the clutch. The good news is that a T5 removes so easy and is only 75lbs so you can even do it in your driveway. Basically drop the mid pipe, remove the shifter, unhook the wiring, remove the driveshaft (after draining), then unbolt the crossmember and 4 bellhousing bolts and out she comes.
2000 Mustang GT Steeda build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.