So my wife bought this car new back in 2007 Nissan Altima 2.5 4 banger 251 thousand miles (yes you read that right 251,000 ) literally scares the s*** out of me the way she drives! I have put a new clutch about two years ago in and replaced the hydraulic slave cyclinder while I had it apart. Now some 2 years later seems to have a issue with shifting like someone is fighting against me to put it in gear or sometimes grinds in reverse. I'm thinking the slave cyclinder is leaking or going out but wouldnt explain the stiffness in the Shifter. Any ideas ?

Not an expert,... but Syncros are a weak point in some Nissan Manuals and would fit the symptoms you describe.