Have a look at this wiki for a starting place of documentation.
Level shifters are recommended
See “How to use on Arduino” (almost to the bottom of the page)
Just personal view / comments below:
I don't want to start a debate, just another viewpoint..
A series resistor is not a level shifter per se. It is a current limiter.
This would not be a recommended way to 'level shift' (still turning on the ESD clamps)
MISO (Master In Slave Out) would not use a resistive level shifter. (you said you put resistors on n data lines)
My concern is that since you have already ran a 5V signal on the bus to the board, you have subjected components to electrical over stress.
If you have induced damage, further attempts to configure this board are a fruitless / frustrating effort.