How do I COLOR with a lot of lines, strokes, paths, & imported drawings

Title edited for brevity by moderator. Was:

"How do I COLOR with a lot of lines,strokes,paths, & imported drawings all in one huge project? FACING A DEADLINE FOR A CLIENT! Thanks for the help!"

Okay so i'm in a pinch & I have to meet a deadline for the most intense & biggest Illustrator project that I have ever done (image below). I have an album cover art I am working on for a client. It is him (my client) at a "claw machine" in an arcade. Inside of the claw machine is multiple items, such as a, stack of money, a midi drum pad, a studio microphone, expensive glasses, etc. I will post a picture of my current state attached with this thread. I recently finished the linework & now it is time to color. Normally I never have any issues coloring, but this project is huge. A lot of layers, paths, strokes, lines, etc. The items that are going to be inside of the claw machine were drawn up separate inside of a different Adobe Illustrator file. My client sent me a photo of him really at a claw machine. So I used that photo & pretty much traced it. Hyptothetically speaking, I could color that easy peezy & call it a day. The problem I have is the custom items we are putting inside of the claw machine, that the original photo, of course, did not have. So what I did, like said earlier, I drew them up separately. I colored them separately (& now im thinking maybe I shouldnt have. maybe i should of only imported the linewor & not colored them separate). There was a total of 6 custom items going into this claw machine. I dont think it matters but once I finished the linework on the original image of my client & the machine, I then, imported each of the 6 items, individually, into the main project. I organized the linework layers to be on top of the items because later down the line I am going to have to color over the extra items on the edges becuse It will not let me splice them in advance. Because of the walls & windows on the claw machine, in a 3D world, Ideally, your only going to see half of the item or prize. especially from a side, angled view. So in the image below, understand that I also have to get some of the "item images" cut in half or even less. but now that I finished placing everything in its place I cannot figure out how to color this bad boy. I tried...

Expand>

Expand Appearance>

Merge>

Rectangle tool>

Color>

Send to back>

Highlight>

Merge>

Isolate selected groups.

This process deleted out half of my image, which has never happened on any other of my ordinary drawings. Mind you I did color the 6 items individually just fine. I also want to mention that I am a beginner with Vector Art. I am more of a Photoshop guy. Thats where I work the most & with pixels. Once in a while I get a cartoon request from a client that will requre me to use Illustrator for the most part. I actually really like Illustrator. I just dont know enough about it to always make happen what I want to make happen & it becomes a little frustrating. I am figuring that I cannot color because of something I did wrong when Importing these layers. I did it by copy & pasting the images onto their own layers. Then I dragged those layers into the group section of my original image. It wont let me use Live Paint. It wont let me use the knife tool. It would not let me Expand & Divide. I thought if I did that then maybe I could delete certain paths as overstrokes. But it did not work out in my favor. It ended up deleting many paths. Ive looked on Google over & over. I cannot find anything or anyone having the same issue as me when working on big projects with a lot of layers. If somebody could please help me out with some advice I would really appreciate it. I do not want to tell my client I am having coloring issues because I feel it is unprofessional. This is the only place I had left to come. Thank you in advance for your help

(side note: my computer would not translate my layer panel into the screenshot & i have no idea why. I tried to get the layer panel in there for you guys)