Well, I've never done this before as I've always followed how the EA item I cloned is set up, but I think it's possible to force a mesh group to use a different texture. It would involve doing what's in
this tutorial.
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Edit: Ah! I haven't been sleeping well and am not thinking clearly. I just remembered that there are at least two ships in the Get Famous expansion pack that uses five diffuse textures. The ships have five mesh groups, as well. You'd need at least two mesh groups--one for the main portion of the helicopter and one for the windows. The thing is, if you use a mesh from an expansion pack I think only those who have that expansion pack could use your item. You'd have to make it base game compatible.
Regardless, the instructions written below might help you. Or not.
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Keep in mind that there may be a better way, but here is how I'd handle your project.
Clone the Home is Where the Hutch Is. It has two mesh groups (which is all you need, really, since you'd need just two shaders) and uses two diffuse textures, as well as two specular maps and two bump maps. Plus, it's a floor item.
Combine all of your textures except for the texture of the windows onto one big DDS or PNG file (If DDS no alpha is necessary and save as DXT1 No Alpha). I think the biggest you can go is 2048 x 2048 pixels. Any bigger and I'm pretty sure Studio will resize it to 2048 x 2048. Currently, the texture for the helicopter is 1536 x 1536. That won't work. The only way you can get a big texture to work is if you're using the HQ mod and even then I'm sure the biggest you can go is 4096 x 4096.
I don't know what size you'd need for your texture as I don't know what size the other textures are. You didn't share any textures other than the one for the body of the helicopter. You might need 2048 x 2048 or you might need 1024 x 2048. I don't know. I'd have to see your textures. However, to give you an idea of what I mean here's a screenshot of four textures combined into one. This was for a ship from the game that someone was editing.
Put your windows' texture in another image. I don't know what size you'd need it. Possibly, 1024 x 1024 or, more likely, 512 x 512. This one
will need an alpha channel as the helicopter's windows are meant to be partially transparent. Make your alpha channel grey. Darker grey = more transparency; lighter grey = less transparency. Black = full invisibility; white = fully visible. You need a DDS for this. Save as DXT5 Interpolated Alpha. So, you'll have two diffuse textures. One for the windows and one for the rest of the helicopter.
Open your helicopter in Blender and first, get that polycount down! I cannot stress this enough. It is
way too high and will cause game lag. Lower the polycount on each mesh group. Try to get the whole mesh with all of its mesh groups under 50,000 polygons. Even better, get it below 25,000 polygons.
Select the flat plane meshes and delete by pressing X.
Select the wheels, edit mode, move UV islands off the map. Select the mesh group with the windshield wipers, etc. Edit mode, move UV islands off the map.
Join all the groups together (Select all mesh groups, Ctrl + J).
Edit mode, face select, select one face in each window. Ctrl + L and all of the windows will be selected. Press P to separate. You'll have two mesh groups now.
Select the helicopter, edit mode. In the UV editor press A to select all UV islands. In the UV editor, go to Image > Open Image and select the texture you made. Doing this in the steps I described will assign your mesh to your texture.
If your UV islands are stretched, press A to select them in the UV editor, the S to scale, then Y, then .5.
In the UV editor, enable Keep UV and Edit Mode Mesh Selection in Sync. Switch to face select. Now you can see the UV islands without the need to select the helicopter.
In the 3D window, press N to open the side panel. Under Shading switch to Multitexture. Now, you'll see the texture on your mesh (see the arrow with "59" under it below)
Move the UV islands that are off the map back onto the map. If you've done the above, you'll see the texture on your mesh in real-time as you're moving the UV islands. Place the UV islands on the map so that the texture matches up with the UV islands. You may have to scale the UV islands. Press S in the UV editor to do so.
Go into object mode. Select the windows. Edit mode. In the UV editor, press A, open your windows' texture. Place the UV islands so that they match up with your texture.
Save your file. Close Blender or start a new file.
Open the hutch in Blender. Append your helicopter mesh. The image below is from another tutorial I'm writing but it shows the steps needed. File > Append > navigate to your file > Object > Shift-select the two mesh groups (they'll be called S4Studio_mesh_something) > Append from Library. Delete the bone_bone_shape and the extra rig.
Assign the helicopter body a cut number of 0. Give the windows a cut number of 2. Delete the hutch and the hutch's glass group as you don't need them anymore. Keep the flat plane that's for the floor shadow.
Select the floor shadow mesh. Go into top view by pressing Numpad 7. R to rotate then 90 to rotate 90 degrees. with the floor shadow still selected, edit mode, S to scale it bigger. You can scale it on the Y-axis with S, then Y, or along the X-axis with S, then X. You can move it with G. Constrain the movement to the Y or X axes with G, then Y or X. Do not raise or lower this mesh. Position and size the floor shadow how you want it then save. This is your LOD 0.
Reduce the polycount using decimate and/or dissolving edges (select an edge, or you can hold Alt + Shift to select an entire edge loop, X, then dissolve edges). Save. This is your LOD 1. Do the same as you just did for LOD 2.
Open your LOD 0 and delete the floor shadow mesh. Select all of the remaining mesh groups then Ctrl + J to join the groups. Give it a cut number of 0. Save. This is your LOD 0 shadow mesh (this mesh is for sun shadows when your object is outdoors). Open LOD 1 and do the same, then again for LOD 2.
Import your meshes and your two diffuse textures.
For your bump maps, follow what I wrote
here. You need a bump map for the helicopter and one for the helicopter's windows.
The specular map depends on what kind of shine you want on your object. In a specular image, the red, green, and blue channels all control different things. You'd lighten or darken a channel depending on what you're trying to achieve. The alpha channel controls how intense the red, green, and blue channels' effects are. Black turns off the specular and white gives you the most shine. Grey creates an in-between effect. The easiest thing, I think, is to clone an EA item that has the sort of shine you want (you may have to clone more than one item) and do what EA has done. It's best to use a DDS for this as it can support an alpha channel. A PNG cannot support an alpha channel so it uses transparency in the PNG itself to create effects, and that's tricky to get right. A DDS is easier. Save as DXT5 Interpolated Alpha. You'll need a specular for the helicopter and the helicopter's windows.
In the end, you should have three LOD meshes, three LOD shadow meshes, two diffuses, two bump maps, and two specular maps. You can import the specular and bump maps through the warehouse. You don't need to worry about changing a shader since the hutch already had a mesh group using the PhongAlpha shader. You just swapped your window mesh group with the hutch's glass group.
That's it! You're done!
Ideally, you'd want to clone a decor item with four groups since your mesh is currently divided into four groups, and you'd want one with three diffuse textures since your UV layout is designed around three separate diffuse textures. The trouble is I'm not aware of any decor items that fit that description. The Tall Bath Cabinet has three mesh groups and two diffuse textures. Two of the mesh groups are PhongAlpha and you need just one that's PhongAlpha but that's no big deal. Changing the shader is easy. 
