To "project" anything drawn in-the-flat onto the top plane of an isometric cube:

1. Rotate the artwork 45°

2. Scale to 100% horizontal, 57.74% vertical ( because .5774 is the sine of the isometric angle, 35°16'').

So in your diagram, you can save yourself some time by drawing the whole thing in the flat (all the base circles and the connector lines), selecting it all, and performing the two steps.

With circles, the advantage of first rotating to 45° is that the anchorPoints of the resulting isometric ellipses will be oriented on the isometric axes, providing snap-to locations for alignment to other isometric edges. Alternatively, apply Object>Path>Add Anchor Points to the circle either before or after the vertical scale. That will add anchorPoints at the middle of each segment, and after scaling vertically, you'll have anchorPoints at the major diameter, minor diameter, and isometric diameters.

If you then want to use true proportion for the height of the cylinders, move copies of the isometric ellipses vertically a distance of true measure multiplied by .8165—cosine of the isometric angle—(or scaled to 81.65% vertically).

Example: Assume you want a properly-proportioned cylinder of diameter 1.25" and length .375".

1. Draw a 1.25" circle.

2. Scale it vertically 57.74%.

3. DoubleClick the black pointer tool. In the move dialog, key your true-length measure (.375), followed by a multiplication symbol (*), followed by .8165. Then cllick the Copy button.

4. White pointer: Select the bottom anchorPoint of both ellipses. Copy. Paste In Front.

5. Press Ctrl and tap J twice (shortcut for Join). That gives you the side of the cylinder, to which you can now apply a horizontal linear grad.

So you could draw that whole diagram in a matter of minutes and end up with properly-proportioned heights (if it matters), and end up with clean & tidy path constructions to which you can apply ordinary linear grads, instead of having the possibly hundreds of paths which 3D Effect will ultimately produce.

On the other hand, you could also simply go ahead and use 3D Effect in its Isometric Top preset orientation, for each of the differently-shaped objects. Then store them as Symbols. Then stack and arrange Instances of the Symbols to construct the diagram.

Example: Assume you want to draw the object that is labeled Supplier in your screenshot in numerical diameter-to-height proportion, with diameter 1" and height .5".

1. Draw the green, blue, and orange objects in the flat. (Radial Grid tool would be handy for this.) Give them solid fills, no strokes. Group them.

2. Proportionally scale the set of circular shapes to 72 pts (which is 1").

2. Effect>3D>Extrude & Bevel. Select Isometric Top from the popup menu. Set the Extrude Depth to 36 pts (which is .5").

3. Drag the result to the Symbols palette.

4. Arrange as many instances of the Symbol as needed in the diagram.

In other words, as long as you measure dimensions of the base paths in points, the Extrude Depth setting in 3D Extrude & Bevel is proportional.

JET