First off, I've never done it. However, I bought a video for doing a 5FSE engine swap (Gen4) in which he takes off the intake, fuel rail, and more, so he can leave behind the harness. I decided not to do it that way, but here's what I can tell you...
Intake manifold is basically held on by 6 bolts and 2 nuts. Pic below shows 6 bolts. You're going to have to get to them from below. If you try to come from directly below, you really need to pull the passenger cv axle to have any chance. The guy on the video got to them from further back down the body using about 3 feet of extensions and a swivel socket, plus he had the luxury of a lift rack. The arrow points to where the Vacuum Switch Valve (VSV) for EGR should be mounted on a bracket. It'll be in your way if you come from directly below.
Nut on right side... Looks like you can get this from the top. The one of this engine was missing. I put something on there for this pic. You might want to remove the ground wire bolt above it, but it shouldn't be too hard to get to.
Nut on left side...
More on the left side... The guy gets to the nut (green) by removing the metal pipe that connects at the head (red) and runs up to the EGR valve. Its got to come loose anyway to disconnect the intake from the head. He makes it easier by removing the throttle body in order to get to the top bolt (blue, bolt missing!) of the black plate which hold the coil packs (I'm sure this is different on your Gen3). The plate is mounted on the head with more bolts that are easy to get to. Of course that whole side of the engine is easier to work with if the air box and resonator are removed and probably cruise control too.
Forum member Fenixus put together a great post on removing the fuel rail here:
DIY Fuel rail & injectors removal - 4cyl i4 5s-fe gen4 camry - PICS !
Good luck.