Let's take this one at time.
diminishing the clunk when shifting gears may be as simple as adjusting the throttle cable. That made a big difference to the same problem on my brother's 91. About a 2 minute job. seriously. if you want instructions post back and I will tell you how.
next, I woudl try new fluids. Drain the tranny (don't flush unless the flush machine uses the trucks own pump) and the transfer case fluids and replace the fluids (ATF and diff oil respectively)and make sure the level is right when hot and cold on the tranny. see if that helps. take note of what the fluid looks like when it comes out.
Next, lube the drive shaft spider/u joints (4 zircs) but not the drive shaft itself. (There are threads here on drive shaft clunks that explain why not to lube the drive shaft using the zircs). Try to lift and move each end of the drive shafts and see if you have any play in the u-joints.
Also, check the phase alignment of the u-joints to each other at either end of the drive shaft. the U shaped arms at either end should be lined up with each other for the rear drive shaft (e.g., "--" and "--") and perpendicular for the front drive shaft (eg, "I" and "--"). Based on a recent thread here I just checked mine and they were wrong for the front. This can cause vibration. Since your pinion shaft was done, maybe they misaligned your front drive shaft when they reassembled. Apoparently "out of phase" is counter-intuitive to your average wrench.
so far this is Mr. Lube knucklehead territory. You have spent about 15 minutes of your life and $25 at mr lube on good preventative maintenance.
next you want to drop the drive shafts, separate the drive shafts into its two parts, lube the splines where they join and clean out the old grease in the part that receives the splines. This requires unbolting the diff ends of both driveshafts (8 bolts). There are more instructions in the other threads I mentioned on how to do this. Optionally, a mechanic should be willing to do it for well under $100. It is not a lot of work and it should be done at your mileage to allow proper expansion of the shafts and avoid loading problems with the diffs and t-case.
If none of this worked then I guess I would start to consider the front pinion as the problem as wlel as every part in the system but I would not be so certain the pinion is leaking or that a new seal will fix the problem. lots of stuff ends up dripping onto it, especially with a 3FE with 128k over top of it. I would monitor the pinion seal closely and clean it regularly until I was sure it was failing and that what I was seeing was not motor oil or some other fluid from above or nearby.
Even if the pinion seal is leaking you might get away with just changing the diff oil in the axle (mr lube again) and unplugging the diff breather hose. that's a little rubber hose sticking out of a brass fitting on top of the driver's side of the axle. There is a write up in tech section here on how to extend this hose. You don't need to extend it but do clean it because if it blocks up it can pressurize the axle housing causing diff oil to seek to escape elsewhere. This is a bit of a gamble mind you, but still good preventative maintenance if it doesn't work.
As for the birfields, a single clunk does not necessarily sound like a birfield problem as others have already said. here is a test. point truck uphill. turn steering wheel full lock. Gun it to complete complete a 90 degree turn. Turn steering wheel full lock the otherway. Gun it again. Then try turning 90 degrees uphill at 20 mph both ways. This puts maximum stress on the birfs. Repeat any test if you get a click or clunk. If you hear a consistent clunking noise coming from either wheel at any time during these tests you probably have a birf issue, but it should be more like a series of pops. If all you get is an occasional clunk it might be a very minor birf issue but I would also suspect some other part of the suspension. Take it to a good alignment shop and ask them if they can see what's wrong.
Even if you do get popping from the birfs, it does not mean they need replacing. They can run for years with a pop or clunk. You said the inner axle seals were replaced a few years back. That means they repacked your birfields with grease but you don't mention why. If a repack is delayed too late the birfs are damaged and continue to clunk after the repack. However they often don't seem to get worse once they get fresh grease so unless you are using oversized tires or rock crawling you are still unlikely to break the birf and will get fair warning in terms of progressively more clunking before you do.
of course, they might have screwed up when they redid the axles seal (ask me how I know). There is no way to know for sure but you can take a look at the exterior surface of your knuckle housing (the bowl shaped thing on the inside of the wheel housing). if it is bone dry or is covered with runny stuff (e.g., grease mixed with diff oil) then that is a sign of no grease in the axle housing or optionally a failed inner axle seal. Don't prejudge what causes the latter. The inner oil seals can wear a groove in the inner axle that leads to quicker failures after replacement.
