Is this the stock clutch master cylinder. I am asking because the clutch seems to be a bit late to engage. I really have to press it all the way to the floor. Also it only seems to have one bolt hole that lines up.

 

Can't see the clutch master in the picture. It is directly under the brake booster. If your refering to the resivoir only having one bolt hole line up, I've always seen it mounted on a bracket that bolts to the brake booster.

Heres a picture of my car. You can see the bracket on the booster. Where your resivoir is at now is where the fan and fuel pump relays normally are (I think its these relays).

 

My mistake I thought the rest was hidden in the wall I am use to them being one solid unit.