It took me also a long time to figure it out but: instead of run/jump/grab: move him close to the edge, then execute a forward roll and Indy rolls neatly onto the next ledge. (It is possible that you do not make it to the ledge but you have to find the right angle to make the forward roll) Use this manouver to move from ledge to ledge. It's safer and more precise than a running leap.
Resumé: You start in Aetherium, swim forward and land on bleu ledge, walk forward to the edge, turn around and drop into the ether. Turn right and swim out of the Aetherium (ether) onto the ledge. Than you do what I wrote above. Than dive into the ether and turn left to see the tunnel with green stripes. Swim to the end following twists and turns. You end up in a blue room. Take a running leap to either of the blue platforms ahead. Pull up, walk to the orb-like object and take that "Tool from Beyond". Hop back into the ether and swim down the green tunnel to where you entered then turn left.
I hope it works out well. Succes!
[This message has been edited by Monique (edited May 21, 2000).]