Having just done this on my '60, here's some things I picked up while doing mine:
1) soak/drench all parts to be removed with a penetrating oil i.e. LiquidWrench, etc... prior to even trying to move the parts -- bushings too, especially at the shackle/bushing connection. The oil will soak into the cavity between the bushing and the shackle pin and help break the rust and lube it for easier removal
2) place the end of a medium sized pry bar (about 20-24" long) inbetween the bushing and the shackle plate and apply pressure while tapping on the protruding pin threads (assuming that you won't be reusing the shackles - HIGHLY recommend replacing with greasable pins and shackles as the difficult removal of the old ones is probably related to heavy corrosion of the pins). If tapping on the threads doesn't work, loose the pry bar and try driving the plate off with blows from a 4-5 lb. hand-held sledge hammer. Placing a short length of 2x4 against the plate and hammering that allows for direct transfer of the blow to the plate if you can't get the head of the hammer directly on the plate itself.
3) if the above fails, grab a propane torch and heat the s#%t out of it, fry the bushings, etc... and then try the prying/direct hammer techniques again. Had one stubborn shackle that wouldn't respond to anything until we super heated it and expanded all the parts -- it came flying off with the first blow of the hammer.
4) once you get it to move out enough to get your fingers around it, you might be able to just reef it out by twisting and rocking it back and forth as you pull. Some of mine were actually easier to get out by this method once they got started with a little persuasion from the above techniques
5) my pins came out easily with no load placed on the spring. The shackles however, required some manipulation with the OEM bottle jack placed under the leaf assembly, just forward of the axle housing, raised slightly to put a slight deflection in the spring arch (flattened out). I just played with this relationship using the jack until the tension between the shackle and the spring became neutral, and took the pressure off of the shackle pin allowing the shackle plate to be driven out easily. Same goes for the install -- bottle jack was the key tool for an easy install.
6) don't reuse your old parts, especially if they show any signs of corrosion. The greasable shackles and pins from Man-A-Fre or Spector are worth their weight in gold.
7) muffler issue: had it on the '60 as well. Disconnect the muffler hanger bracket at the very rear of the exhaust, near the tailpipe. If that won't give you enough play to pull the pipe down out of the way, then also disconnect the hanger bracket/strap just aft of the muffler. Once I had disconnected both of these, I was able to pull (with some muscle) the tailpipe down far enough to access the shackle plate/nuts and without compromising the welds on the exhaust system. It won't stay that way -- you have to hold it down out of the way while you drive the plate out so another pair of hands is really helpful.
8) grease the inside of the new bushings and the pins of the new hardware well prior to reassembly which helps quite a bit and saves damage to your new bushings
Hope it helps,
-dogboy- '87 FJ60