My guess would be a mildew/moldy odor. Looking at that picture you can see that the entire floor board has had water in it at some point. I've seen on TV on one of the car restoration shows where that had one with such bad odor from rodents and whatnot inside that the only way they could get rid of the odor was to acid wash it.

If water has gotten it it could also be in the insulation on the back of the door panels. Or as mentioned, the headliner. I'd look for some sort of chemical or cleaning product that can permanently remove odors. Common things should work though like vinegar, citrus like lemon, baking powder, etc. The vinegar will stink terrible when using it it but it does dry odorless. Personally I'd try spraying everything down with vinegar (and maybe add a couple of drops of citrus oil to make the vinegar tolerable while spraying).

 

I also wipe my interior down with diluted white vinegar (2 parts water, 1 part vinegar) especially on the inside of the window seals in the corners of the windows where stuff likes to grow sometimes when she's not been driven in a while.

 

I sprayed it for 3 consecutive days with vinegar and washed it out... will stop doing this tomorrow and will close it for the weekend to test it.

I put some nylons all over he insulation and the front panel and still had the same odor... I don't think it is coming from there but if it remains, yes, I will remove them as well to spray them as well. check some photos attached



I sent it with the carpet to the DRY CLEANING SHOP.

 

You did this without any problems? can I spray it on the leather seats? what do you think?

 

How easy was it pulling the somewhat fragile headliner panel out the back? I really want to pull mine out to get it redone and use the opportunity to pull the sunroof out and try and fix it as well as run some wires.

 

A 20 min job... easy and simple! you just need a second person at the end to help you getting it out.
you need to deform it a little bit at the end to get it back

 

The headliner on the 08-09 Hummers are much sturdier. made from different material than the older models.

 

Ah.... good point. I did not even think about the fact that theirs is one of the newer ones.