I am trying to fill in the bottom most layer of the body (or fill it with my darkest color), yet every time it fills the entire selection box instead of the area inside of the selected path.  Also, for a reason unknown to me, many times when I attempt to fill in a selection I can use every color except for white?!  I have attached a screenshot of what I am experiencing. 

In the screenshot, the selection box looks much bigger than the path.  I would guess that you don't have the path selected, and that you have something else selected instead.  Or possibly there's a filter there?  But it's hard to tell from the JPG.  If you could provide the SVG file, we could probably be more helpful.

Oh, also, you have a blend mode applied to that layer (Multiply).  So any kind of color is going to be wonky.  If that layer is where you're having trouble making it white, that could be the reason.  Otherwise, I would ask what does happen when you try to fill something with white?

I'm not sure if the blend mode would be part of the problem filling the path.  Possibly.

Thanks @brynn What’s weird is every time I click to select the path that selection box appears as well.  Also, I went ahead and changed the blend mode back to normal, but unfortunately it didn’t help the issue I am experiencing.  I have attached an updated screenshot.  

When I try to fill something in white, it does nothing as if there was no fill at all and many of the ones giving me problems also have discolored boxes around them aswell.

What is your prefeed method of me sending over the SVG file?

You can attach it to your message, just like the other one above.  Or you could upload it anywhere you like, and just post the link to it.  Whatever works best for you.

Check all your layers for the blend mode.  Anything except for Normal in the layer blend mode could potentially change your colors, even if it's just one layer.  Also, if you have moved any objects from one layer to another, while that layer had a blend mode, that object gets assigned a filter of the blend mode, so that no matter which layer you eventually put the object, it still has the blend mode.  So you might have to check for filters applied to things that were in that layer, and remove the filters.

The oversized selection box reminds me of what we often see with a filter.  They often make the object larger (usually because of blurs, but other reasons as well).  I'm not sure about the fill filling the selection box, but I can investigate when I can open the SVG file.

Ok, I have your SVG file.  I see that you have removed the blend mode from all the layers.  But there are 7 objects in the file that still retain the blend filter.  If you don't have a reason for using them it would probably be better to remove them all.  Because they will affect the colors.  You can do that quickly by Select All, then Filters menu > Remove Filters.

I have not found a way to select the yellow body object, which shows the bounding box like in your screenshot.  It could be that you made some other changes in the file, besides fixing the layer blend modes.  But as far as I can tell, you should be able to change the colors of that object, after removing the last filters.

Another thing I noticed, is that for some objects, you used a Swatch for the stroke color.  But the stroke has zero width, making it invisible.  So if you don't want the stroke, you can remove it entirely, rather than make it with zero width.  (It doesn't make any difference to how the image looks, but it makes a cleaner, leaner file.)  You can remove the stroke entirely, by clicking the big X button in Object menu > Fill and Stroke > Stroke Paint tab.  Or the tiny X chip at the far left of the palette, while holding Shift key, will remove the stroke.

In your original description, I thought there might be some clipping that was part of the problem.  But I haven't found any clipping or masking in the file.

I think after removing the last filters, everything will be fine.  But let me know if you still have problems, and I can look deeper into the file.

Edit

Also, I meant to mention that the yellow body is partially transparent.  So that could also affect the color that you see.  So you might want to make it 100% opaque.

Thank you @brynn that was very helpful.  I am still experiencing troubles with the transparency of the body object.  Both the Alpha (opacity) and opacity levels are 100%, yet I am still seeing a transparent object.

What happens if you do filters>remove filers and path>remove path effect?  It's hard to tell what is happening to it without seeing the actualy svg (vs the attached jpg).  I'd also try path>break apart.

HI,
On the png it says that the selected object is filtered. You can see that at the bottom of the jpg.

Thank you @Kirstie I had origonally done what @brynn had suggested and selected all an through the Filters menu I removed all filters, I guess I needed to apply that to the object.  I am back on track, thanks everyone.