Here is an interesting link to a scientific analysis of K&N air filters.
http://tinyurl.com/26ez9
I agree that you will not be able to gain significant horsepower increases with exaust and air filter mods. Not the kind you are looking for for towing your boat. I however commonly tow a 1600lb (empty weight) trailer with up to 1000lb of cargo with my FJ62. The 62 without a trailer will slow to 50mph on long steep grades and with a trailer it has trouble with hills. Conservation of momentum comes to mind, like I used to pracitce in my air cooled vert beetle before hot rodding the heck out of the motor.
With the auto tranny in the FJ62 on flat runs I could easily tow up to 2600lb at 70mph. The problem is with the A440F automatic trans and the cusp between overdrive and 4th gear. It's similar to running 33" tires without a trailer, you wind up back & forth between overdrive and 4th on any hill or against the wind. The A440F robs lots of power from the 3FE engine. I converted my truck to an H55F 5speed manual gearbox which allows me a lot more control of how I apply the power. The overall final drive ratio is shorter than the A440F but perhaps taller than the 4 speed in the FJ60 despite the rack & pinon difference.
As for better breathing you could have some porting and polishing work done on the head but that alone will not get you a significant increase in power. When I rebuilt my 3FE I went 40 over on the pistons, installed perfect circle rings, and had Jim Chenoweth work over the cylinder head. He installed Chevy SS valves and did some porting and polishing. I had the rotating assembly balanced as well. All that work resulted in a noticable increase in power. Nothing significant but noticable. I equate it to the increase I got when I had preveously installed the Flowmaster muffler and a K&N air filter.
I did get a significant power increase with the overbored throttle body that I just installed. At least 4 times the difference I noticed from all the other mods combined. RC Engineering overbored it by 3mm and installed a new butterfly valve. I have not had a chance to find a grade to pull, it's flat as hell around Houston, but that will be the true test for towing ability. I have realized a significant increase throughout the power band. In 2nd gear it will put me back in the seat when I mash on the foot feed.
Of course an overbored throttle body will not do you any good on your 2f unless you also fuel inject it. That being said, there are ways to get more power out of these engines without killing them or loosing torque. If the FJ60 were mine I would have Jim C. rebuild the carb and drive it. Go ahead and pull your boat and see if you can live with going slow. If other drivers are throwing rocks at you look into a different tow vehicle or drop in a SBC. Going slow sounds a lot cheaper though.
I am no automotive engineer but would love to see what a 2F would do with 3 WEBER DCNF side draft 2 bbl carbs and a 2.5 inch exhaust would do. My beetle displaces only 1904 cc but runs like a banshee on crank with twin 44mm 2 bbl Weber carbs and moderate cylinder heads. Thats a mild upgrade in VW terms, the guys displacing 2180cc and up have the front wheels in the air on launch. Our TLC engines are tractor motors, but motors none the less. They pump air and if you make them pump more air they make they more ponys. These guys make a living out of hot rodding inline 6 cyliner engines:
http://cliffordperformanceshop.com/site04/home.htm
I digress, ... go ahead and pull the boat and flog the dog crap out of the 2F. If it aint enough add a SBC or buy a turbodiesel tow rig.
Good luck