All would be easier with the engine out. Like I said I was worried if I'd installed the alternator whole assembly was out, I wouldn't be able to install the ac lines. But that wasn't the case. There's enough room under the alternator installed, to install the two ac lines. Definitely easier to install axles while out.

 

I just caught up on this posting tonight, sorry I missed your earlier questions. I'm just finishing up an engine swap on a 2001 Highlander so I have some more info to share. I'll get my pictures sorted out and post them shortly.

 

FYI tim73
The engine I just replaced in the 2001 Highlander I'm working on has the same type of engine mount/oil pump and tensioner as the jdm engines. This mount is the same in the USDM highlander, Like the first picture I posted earlier in this post. I believe this engine was out of a Kluger which is the Japanese version of the Highlander. It was in a right hand drive vehicle by the configuration of the wiring harness.
Like you already discovered the vacuum line to the brake booster comes of the passenger side of the intake "log". I drilled and tapped the the boss in the jdm intake to accept the 90 deg vacuum connector to feed the brake booster on the driver side and swapped the plug for the passenger side.
I installed a new timing belt kit and water pump even though the belt looked to be in good condition.. I tried using a timing belt from Autozone and it made a weird noise when the printing passed over the idler pulley. Pulled it back off and installed a Toyota belt tonight and all is quiet again. I will stick with the Aisin kits from here on out.
The engine on the Highlander came out the top without too much trouble which has me thinking. The next RX300 I get I'm going to try pulling it out the top also, after removing the wipers/pan assembly.
I've removed the cowl and pan 2 or 3 times now on the RX and it is easy peasy.
Some pics for documentaion
Cheers

 

Seperating old usdm from transmission.

had to take off the passenger axle, couldn't figure out a way to seperate the engine from the mounts due to the guide pins wouldn't clear.

 

but, you probably already know that or figured a way around it.