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One of the first things you should do is provide a connection for the scope probe ground.  If you think you'll be regularly looking at signals on this board, then one of those little loops or pins to clip a scope probe too would be useful.  If it's a one-off problem, then just a thru-hole pad would be good enough.  You solder a small ground wire to the pad, then clip the probe to the other end of the wire.

The high-speed signals are different.  At these speeds, you are probably delay-matching the data lines.  You want something that doesn't interfere with the delay.  Unfortunately, there is no such thing.  In this case, looking at the signals will affect them.

I might add one of those clips to the clock line only.  That way you can see the clock signal hands-free.  Then manually hold the probe for the other channel to whatever data line you are interested in.  I'm assuming you can arrange for particular read and write sequences to eventually see the skew of every data line relative to the clock.

Be prepared for the skew being a little different when the scope probes are removed.