Welcome to the forum.
First off: there is no magic bullet to raise your fuel economy 25% (16 to 20 mpg is a 25% improvement).
Well, there is one magic bullet, but I doubt you'll go for it: consider getting a more efficient vehicle. Use a trailer to haul your work stuff. I see guys doing that around here.
1 & 2: Don't waste your money on HHO kits or acetone. Search this forum to find out why.
3: can't comment - don't know enough about programmers.
Your driving style has the biggest impact on your fuel consumption. Get yourself a fuel consumption display (ScanGauge, ultragauge or equivalent) and use it to push yourself further in terms of driving. Instant feedback is critical to honing your technique behind the wheel.
The lift kit increases fuel consumption. The muffler delete may also be hurting (negatively affecting low RPM torque, where you want to be operating the engine for best MPG).
Gearing: the taller the gearing (lower engine RPM), the better, provided you can hold top gear at cruise in your normal driving environment.
A tonneau will help aerodynamics. It will be a marginal improvement (most mods will be marginal). Synth in the rear end will help, again marginally.
I take it you've looked at these:
65+ Efficiency Mods
100+ Hypermiling Tips