How to stabilise SPI connection
If you leave the chip in place you will encounter major problems.


You have to supply power to the chip, but the powers supply is likely to be connected to all devices with the same supply voltage. e.g. if you connect the (3V3?) supply you will supply all 3V3 chips on the board. You have no idea what that will do to the board, as it will only be partly powered. 
The I/O pins will be connected to existing chips. If they are powered they will try to drive against your signals. If they are un-powered you have no idea what the behavior is of the ports. 


There is no use trying to read the chip in-situ. You have to isolate the input pins. The MISO should not be a problem. If you don't care if the rest of the board survives, you can just pump in enough current till the supply voltage is correct.