Re java skills:I checked the damage progression on cs and it's not viable. The best secondary skills for a java seem to be imo multi shot (far better range than strafe) and immolation arrow (no timer, 25+ sec duration and the dot stacks so can do real damage IF you can keep your target still). Strafe is ok too, everything else does too little damage, at least without great gear, though fend could be viable. Looks like best way to deal with bosses is 1 pt guided with a fast bow and switching helm to gface. Particularly effective with baal as you can ga around a pillar safely.
A bow w/knockback is good for this, so the Amazon specific bows or a Kuko soceted w/Nef work. "Death" runeword is woking well for me in an Ashwood bow with +3 skills, since the bosses don't flee. IA works great if you can back them into an obstacle and keep them in KB "lock". My A1 merc has Riphook socketed with Nef, so that's a big help as well. FA is another good option for the classic LF/FA build.
I don't know why you would run Baal in 1.07--his drops are garbage and he's dangerous. If nothing else, he tends to drain the bank account for merc ressurections.