Please forgive me for this long winded post.

Who I am:
A friend of mine owns a fairly large car dealership and is having trouble with HVAC. He's not a technical guy and has asked me to give him a hand in evaluating contractor proposals in hopes that we can select someone that is appropriately suited for the job. My background is in computers and I have worked with contractors in the construction of a few small-medium data centers and I have an interest in radiant heat, solar, alt-energy generation, and HVAC.

The building in question:
The business is a two floor building with vehicle storage and the wash / detail shop down stairs (partially below ground). Upstairs there is a large showroom with 25ft to 30ft tall ceilings and lots of glass facing roughly east. Next to the showroom is the service writing department, parts, customer admissions, and the repair bays. To give a perspective on size, the repair area has over 40 bays. I'd estimate that the building is about 145,000 SQ/FT. As you can imagine the building is not an easy one to design for. The wash/detail shop downstairs generates insane amounts of humidity which easily migrates into the vehicle storage area and the showrooms. The service area has 5 huge automatic garage doors that open and close many times per hour. Not to mention the heat brought in with each vehicle that enters for service or when cars are running in the shop.

The current state of affairs:
The existing contractor has been asked to fix condensation leaks, inoperable units, comfort issues, and humidity problems but progress has been slow. For example, I first visited the building about 18 months ago and immediately noted that the computer room was extremely humid and recommended that it be fixed as soon as possible. Jump forward over a year and the room is still hovering in the 75% to 80% RH range but now with black mold all over the walls. The humidity sensor failed at some point in the past and the contractor said that because the unit is no longer in production they can't buy a replacement sensor. When the air handler motor failed (bad bearing) they said that they'd have to have a custom motor wound to replace it and again recommended that the whole system be replaced. It was and off the shelf sensor and a run-of-the-mill 1HP 3PH induction motor that was in stock at Grainger. When the controller started acting up they again said that because the system is out of production they would have to hire someone to custom program a one-off controller and "it might or might not work". Again they recommended buying a new system. I had a local HVAC guy go in and replace the failed unit with an off the shelf controller. The root cause of the problems is that the unit is way over sized for the heat load and there's an issue with OA getting in. At no time have they mentioned either of these as being contributors.

The bottom line is that I don't have confidence in the existing contractor. When I brought this up to the owner he said that the previous contractors had also had trouble getting that system to work and had started but not finished a number of HVAC related projects and he let them go because they too seemed to be in over their heads.

What I'm hoping to get from this forum:
I want to know what type of approach or strategy a competent contractor would apply to designing and maintaining a complex multi-system environment like this. I want to get a high-level understanding so that I can better identify proposals that fall in line with modern design methods. Of particular concern to me are customer comfort and energy efficiency. The cost of utilities is ridiculous and anything that can be done to reduce cost over the next few years is a plus. If that means looking into geothermal or other technologies please mention it. But again, the focus is on comfort and ROI.

If you made it this far, thanks for investing your time. I appreciate any feedback you can provide...