The front tie rods can be re-bent. There is a how-to on one of the buggy sites for using a tube as a sleeve over the existing tie rod to add strength. However, like the front bolt-on bumper, the tie rods were designed as failure points to prevent something more critical / expensive from failing. So, put some thought into anything you want to beef up.
Axles...the best thing I can recommend for axles is to find a set of working axles and run them until they break. New axles, if you can find them, will run you like $500-$1000 EACH. The cheap GMB brand u-joints have had mixed reviews. Avoid the ones with the grease zerk at all cost, as these are known to be weaker. Mods that I've only seen on a couple FL350R's are these:
1. The addition of an extra link from the frame to the rear of the trailing arm. Have to be precise with the kinematics to make sure you've got centerlines and arc of motion in check. This will take some stress off the axle-link.
2. Adding a limit strap from the frame to the trailing arm to either protect the shock from failing if/when an axle breaks, OR, protecting the axle from failing if/when the shock breaks.
3. Rear shock...unless you run a stout limit strap, you can only run with a shock that's the same full droop length as the stock shock. Anything longer (if using the stock shock mount locations) will require the axles to operate beyond their ability, bind, and wear out quickly. Works is really the only simple remedy (but not cheap). I've seen a few rigs where they've added an upper shock mount at a higher point in order to run a different shock.
Front shocks...Works is it, or else do an a-arm swap and use something else. Important factor is that the shocks are valved correctly for the vehicle type/weight, riding type, and rider weight.
If you're dong a ton of jumping, I'd recommend trying to find a FL400R Pilot. The Pilot trans has a clutch in the gearbox than will allow for more flex when your landing and on/off the throttle. However, Pilot parts are even harder to find than Oddy parts!
And for the gearbox...make sure the input shaft bearings are good and tight, as this is a known failure point. Check the box for leaks and check your fluid level (with overflow bolt) before you ride.