Dealer I worked for was a war eagle dealer in 1994. The 542F (what you have) and the 542FLD (low deck) were 2 different boats. Same basic hull but the LD had the low deck. We also sold Duracraft (Noah) at the time, and they made a nice 1542 with a "tall deck"-and it was NOT popular at all-due to the center of gravity being higher, and in such a small hull the boat got real tipsy. You had to hold real still while the boat was at rest. War Eagle boats are really stable but remember it's just a 542. Yeah there have been tons of 1436's with decks on the front (I have had several)-but it doesn't change the fact that a high deck does decrease it's at-rest instability.
In the late 1990's, I had a customer bring me a 542F (like yours) and wanted me to install a low deck. Called War Eagle and told them what the guy wanted, and war eagle told us that it would be much better for the customer to haul the boat down to them and let the factory do the conversion since they are set up for that kind of stuff. At the time, we were at $55 per labor hour, and we figured about 9 hours to do the change by time the cutting and welding was all done. War eagle did it all, paint and everything, for (at that time) $362 as I recall. That was cheap for the amount of work it takes. AND it was done correctly, and done pretty quickly too. Couple days as I recall.
If you haven't already, call Nick at War Eagle directly and ask him about it.
The "cheap" option is to run some plywood across the top. BUT I can guarantee you a couple things. You won't like it after a while and the plywood will rot. If it's carpeted, you don't see the symptoms of the rot and someday you'll climb into the boat and crack/break the plywood. And of course Murphy's law applies....if it can happen it will and at the worst possible time
. War eagle uses layered Aluminum, no plywood, and it's strong as could be. Also has flotation underneath, so if the boat is swamped, it'll still float.
542's are still popular so if Nick says don't do it, you could always sell yours and then pick up a 548LDV and have a lot more leg room. I sure like mine-and I've used all of the "major" brands. It replaces a 542F almost identical to the one you have and the difference between the 548 and the 542 is akin to daylight and dark; at least with the war eagle's. Another option, sell your 542F and pick up a 542LD, same boat but with a low deck.
If you go with your plan, you'll have to stick a couple pieces of material together in order to span the width. Lots of ways to do it obviously, and it depends on what material you're going to use. I've had them at work in the past with 2 pieces of plywood screwed together flush with a 2x6 under the bottom side and that works. The other problem with just going across the top is all the wasted space underneath...and totally wasted. I'd like to have part of the deck hinged so that you can open it up & let it breathe, or at the least get a way to store some tackle under it.