There are possible values you need to solve by adding up numbers, here's the speed-solve for it:

36 - 3333333339
67 - 7777777774
81 - 8888888889
42 - 4444444446
53 - 5555555558
67 - 7777777774

In the training facility two doors are locked by the clock on the top floor. Once you collected the Clock-Needle put the clock to 8:15 to unlock the doors.

After inserting the MO-Disc into the conference room PC you are tasked to activate two timer based buttons among the students terminals, the code varies, the layout of the buttons stays the same among the seats, meaning left and right from the camera angle you enter once you leave the main PC at the front:

0 1 -- 2 3 = Front Row
4 5 -- 6 7
8 9 -- A B
C D -- E F = Back Row

To activate the power from the transformator you need to put the needle on 70 flat, do this by switching the switches to UP, UP, DOWN, UP, UP in that order

When tasked to activate the animal murals on the fire fountain, use this order to open the door:

Deer, Wolf, Horse, Cougar, Snake, Eagle

To free the Leech-Charm from the container combine RED and GREEN fluids from the tanks as Rebecca (best to have her go up instead of billy, faster)

In order to progress towards the Gondola as Billy press the upper button as Rebecca, send down the combination-lock part to Billy and enter the following code via the lock-dial: 4863

When entering the cleaning-facility you will have to solve a puzzle distributing power to all areas, here's which buttons you need to press:

The fastes way I've seen it done went like this:

As Billy:
Push the metal box all the way to the right against the wall.

As Rebecca:
Rotate the grid left.

As Billy:
Push the leftmost wooden box all the way down next to the box behind the grid.
Push the remaining wooden box to the wall to the left and push it all the way down until it's touching the first wooden box that was pushed.
Push the metal box up to the wall.
Get Billy into the small alcove behind the second box that was pushed to the bottom wall.

As Rebecca:
Rotate the grid right.

As Billy:
Push the wooden box in front of you to the far wall.

As Rebecca:
Rotate the grid right

As Billy:
Push the box down into the hole next to the box that was originally there.
Get Billy out of the pool.

As Rebecca:
Flood the pool.

Cross the box bridge and get the Handle.

It is wise to allready mix RED and GREEN fluids on your way through the Gondola part AFTER you freed the Leech-Charm from it's container if you come across them to make the stripping-agent once again. You just need to add the INDUSTRIAL WATER to get the battery fluid.

RED + GREEN + INDUSTRIAL WATER = BATTERY FLUI