This furnace installation does not look correct. However, Im not real familiar with high efficiency furnace installations. This furnace was installed in an enclosed closet, with no upper combustion air vent, only a lower combustion air vent and two return air vents, one of which was installed in the bathroom. I know that each manufacturer has there own specifications, but, just using general knowledge, I don't see how this could be correct.
My question is: Is any of this correct?

If you have make up air in the closet it should work fine(out side air). The inducer motor is what pulls the fresh air in and out the exhaust. What would worry me is a return in your bath room!!

Code calls for both high and low combustion air unless taken outside.
The manufacturer install instructions must be followed exactly since they supersede all other codes.
The instructions for the install directions should have been left at your home. If not the installer is also in violation because every manufacturer and mechanical code require the directions to be left on site. This is both for you and the inspector(if inspected) so it can be determined if the unit was installed to the manufacturers instructions.

Some questions I have

Why was the combustion air not vented outside to start with? (just curious)

Is the area between the furnace and the return air vents panned with sheet metal and are those areas sealed air tight?

The combustion air that is installed would not pass my inspection in a closet unless the closet door would be a louvered one.

T-Top hit this one when he said no return air in or from a bathroom. That is also a code violation and if you read the manufacturer instructions it should be listed as not allowed along with the kitchen.

You really need to address the combustion air situation

Please take a few photos of the bottom of the furnace and the return area between the furnace and grill please post them here along with the gas piping and the electrical wiring and the disconnect switch.

What are you doing for air filtration (air filter) location? Are two installed one for each return or just one main filter?

How about a picture with the lower blower door removed so we can see location of filters?

Thank you for your quick responses.
hvac1000,
I do not have any further access to this furnace, however I do have some additional photos to share and would appreciate additional comments.

1) To answer your first question. This was a replacement furnace for an older FAU, so the lower combustion air that I eluded to in my first post was in the wall cavity takeing air from the attic area (home was built on slab), and I think the upper combustion air was probably installed in the closet ceiling, which has now been sheetmetaled over.
Are upper and lower combustion air vents required for high efficiency furnace units? (open chamber)

2) The return air vents were installed directly into the plenum area below the furnace. This area appeared to be sealed, but was not sheetmetal lined, which would not be required in our area (just a sealed wood framed box).

3) foot note: Would'nt a louvered closet door allow the potential for cross connection of toxic gases to be drawn into the return air just below the closet. Should'nt this closet door be fully sealed?

4) I thought the 2nd return air in the bathroom was a problem, however could you elaborate on the reasoning, code or whatever?

5) Filter was located at the furnace (blower at the bottom of unit), no other filters present. This filter appeared to be some kind of smart filter,as it had a small cord plugged into the frame area.

This was not one of your questions, but T-Top mentioned the inducer fan bring in fresh air, this is confusing to me. I have seen two PVC vents going out to the exterior, I under stand that system. I have seen one vent with a bell shape at or near the termination. I understand the principle of that type, although I don't understand how it works. I don't understand the one in my first post, where you have a short vent pipe that doesn't leave the closet area. Where is this supposed to draw from? the one vent in the closet? The single vent that terminated at the roof had a PVC T type cap with screens on each end.

Of course I welcome any and all input from everyone. Thank you for your time.

Answer to number 1
Since the combustion air was not taken outside the unit has to be treated like all others. 50% hi and 50% low on the combustion air and to how many square inches it would have to be calculated then divided by two then reduce if grills are applied. The grills have a loss of 25% free air flow so that also has to be calculated.

2 raw wood frame box with dry wall is acceptable for return air only.

3 if the return air was where it is supposed to be that would not be a problem.
BUT the louvered door is no problem in and of itself because it is only going to be sucking in combustion air for the burner. How would the return air become contaminated? It is not blowing into or sucking products of combustion just combustion air not make up air UNLESS the house is so tight. Here is a old trick. Cut a 4X6 opening in the supply plenum and let it blow into the furnace area. You will have no negative air problems then.

4 Furnaces do not like hair spray and other products. It eats at the heat exchanger. BUT the real reason is to draw in farts and other nasty spells. With the return air in the bathroom the entire house will know when someone does a popo. Naturally that could also be a early warning system that someone is using the bathroom or you could hang a air freshener in the return air. LOL.

((This was not one of your questions, but T-Top mentioned the inducer fan bring in fresh air, this is confusing to me))

In this setup the outside air or combustion air is not hooked up except for a short piece of pipe and a elbow. Why they installed the pipe and elbow is a good question because it does nothing. This is not a outdoor combustion air furnace to start as it is not connected to the outside. The combustion air is being drawn into the furnace in the burner area and the combustion air is not directly connected to the small combustion air fan assembly. I guess they put the screen on the 90 degree elbow to stop the bird in the closet from getting into the furnace. LOL that was just a waste of time on the installers part.

Toss the smart filter and get a good 3M one. They are a few bucks every two months but they do a great job. As long as all of the return air is passing through the filter it will be OK. Naturally never run the furnace with out the blower door on.

I am not going to go into the electric but there are a few code violations present but I will address another problem. It comes under the cord and plug rules and others.

They used Galvanized fittings and pipe on the gas line. That is a big NONO and a violation of code. WHY? Galvanizing flakes off over time on the inside of the pipe and valve. This will plugs up the gas valve and pilot with debris.

3) How would return air become contaminated?
I was thinking if there was a malfunction or alteration of the furnace system, such as a blocked vent, creating carbon monoxide in the closet area. This could potentially be drawn into the return from around the closet door or if the door was not fully closed. I believe the mechanical code says something to the effect , that the return air shall not be installed closer than 10 feet from the furnace for this reason. (im not quoting the code by the way).

((such as a blocked vent, creating carbon monoxide in the closet area))

It is a Powered vent system with safetys. The furnace will not start up and shut down with a blocked vent. It will lock out on the pressure switch. This is a new style furnace and they do have a better safety system that the old. I am more concerned with the bathroom problem than a roll out condition due to negative pressure.

How about a brand and model number.

You won't have a negative pressure problem as far as the concerns of the furnace. I was concerned about the moister and smells from a return in the bathroom. No danger just the embarrassment from the one coming out of the restroom if the system was running.