Not to disagree with the previous posts here, but the capacity of pontoon boats is not regulated by the Coast Guard. See http://newboatbuilders.com/pages/load.html
So you would not be violating any Federal regulations. It is an American Boat and Yacht Council standard. Manufacturers use the ABYC standard to calculate the maximum capacity which is partially based on load but also partially based on stability. The manufacturer then puts a capacity label on the boat which looks just like the label required by the CG but does not say US COAST GUARD MAXIMUM CAPACITIES on it.
Also, the manufacturer will certainly no longer be liable for any capacity or stability problems you may have. Additionally, in some states it is a violation of state law to exceed the maximum capacities on the label. So if you exceed those you could possibly be cited by a state water cop.
Adding a third log will add some capacity but not any additional stability. Adding an upper deck will definitely change the stability of the vessel. You need to do capacity test based on stability to find out what the capacity should be with a second deck.
The ABYC standard - H-35 Load Capacity for Pontoon Boats is not free. See http://www.abycinc.org
. However the Canadian Regulation is based on the ABYC standard and only slightly different and it is free on line.
In Canada these are covered in TP1332. http://www.tc.gc.ca/BoatingSafety/regs.htm
Section 4, Hull Design Requirements.
Sub Section 4.3 covers Capacity and flotation for multihull vessels, that is, pontoon boats.
The Basic idea is you place weights on one side of the boat until the water covers the top of the pontoon on that side.
The following is from the course I teach on capacity and flotation:
Add weight to the pontoon boat until all pontoons are awash over their entire length.
Mwc = Maximum Weight Capacity =
Total Weight – Boat weight/Square root of pontoon diameter - 2.35 (1.35 for three log pontoon boats)
Persons Capacity By Test:
For transverse stability: Place weights for engine, battery and fuel tank in the location of each item. Add weight on one side of the pontoon boat evenly distributed fore and aft and as far outboard as practicable, within one foot from the edge of the platform, until the top of the platform on the loaded side is awash. Repeat this on the other side. Record the weights for both side.
For longitudinal stability: (fore and aft) Add weights on the platform, with the center of gravity on the boats centerline. They shall be placed 1/4 of the length of the deck from the forward end. Add weight until the forward edge of the deck becomes awash. Repeat this with the weights placed 1/4 of the length of the deck form the aft end of the deck. Record the weights.
The smaller of the weights in the transverse stability test or the longitudinal test shall be used to determine the Maximum Persons Capacity. The maximum persons capacity is 90% of the weight.
Transverse tests Port = 2500 lbs Starboard = 2550 lb (1020.6 kg)
Longitudinal tests Forward = 2600 lbs Aft = 2650 lb (1202 kg)
The lesser of the above is 2500 lbs. 90% of 2500 = 2250 (1020.6 kg)
I think that putting a second deck on it without performing a stability test is foolish if not negligent. And if you do, and determine how many people can be up there, you are going to have to constantly police the number of people on the upper deck. So I would give this a serious rethink.