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It's a fairly simple process once you step back and take a look at it. You only have to remove a bolt/nut, a cotter pin, a castle nut, and the axle nut. You need a 17mm hand wrench, a 17mm socket, a decent weight hammer, a 1/4" or so punch/dowel, something to pry with, like a 8-10" prybar, and (I believe) a 32mm socket for the axle nut. You can free-rent an axle socket from AutoZone, once you give it back, you get your money back.

Remove the axle nut while the vehicle is on the ground, in reverse gear and parking brake set. You will almost certainly need a breaker bar or similar tool for this, and I find it highly recommendable to use a good, strong breaker bar with at least a 2 foot extension on the handle, for extra leverage. Do not remove the wheel until you've loosened this nut.

Jack the car up and put it on stands, blocking the rear tires and ensuring your safety.

Remove the tire and set it aside.

Remove the shear bolt that connects the strut fork to the middle of the lower control arm. First remove the nut, then using a round punch on the flat spot, drive the bolt out of the hole until it is clear of the lower control arm. At this point, you may also choose to remove the clamp nut at the top of the strut fork, which holds it to the bottom of the strut. This is not necessary, but may make the job a little easier for you. If you choose to do this, stick the prybar into the slot of the fork (where you removed the clamp bolt) and wiggle it in both directions as you're spraying with lubricant, until it moves freely, then pull it off.

Remove the castle nut holding on the lower ball joint (after removing the cotter pin).

Use a decent mallet or framing hammer of good weight to literally WHACK the flat spot on the ball joint seat of the hub at a 90* angle to the control arm's length, right where the ball joint seats in it. After a couple good whacks, pull down on it some, and see if it separates. If it doesn't, wedge something above it and put downward pressure on it while continuing to WHACK that flat spot. This will release the lower ball joint without damaging the boot that surrounds it. This is also a good time to check your ball joint for wear and ensure that the boot is good.

Finish removing the axle nut from the axle stub. Place a catch pan under the transmission axle connection points. Place your prybar between the edge of the axle's transmission stub and the transmission casing, wherever you can fit it. Pry evenly and steadily, increasing tension until the axle "pops" out of the transmission differential slightly. You should, at this point, be able to slide the axle easily with a few fingers into and out of the differential, although it may not come out entirely yet.

Being like Stretch Armstrong, push outward with one hand on the front lower corner of the hub assembly, so that it pushes itself up, out, and back from it's original orientation, which will give the clearance to remove the axle stub from the transmission.

If you opted to not remove the strut fork, push down on the lower control arm to clear the strut fork, then lift the strut toward you, as you face the hub. This will allow the axle's shaft to clear the fork. A quick tap with either a hammer or the back of a wrench will loosen the drive stub from the hub, so that it may be withdrawn.

Installation is basically the reverse of removal, except there should be no reason to beat on anything at this point. Grease the drive stub before you put it in, and ensure that the locking ring is on the differential stub, and that it "clicks" into place when you press it in. Give it a good shove to compress the whole axle straight and drive that circlip into place.

Using this method, no alignment is necessary afterward, and the whole job should only take about an hour for a good shade-tree mechanic, about 2 hours for an inexperienced tinkerer.

Torque Specs For This DIY
Axle Nut: 134 F#
Lower Control Arm Ball Joint Castle Nut: 34 F# (reinsert cotter pin after final torque procedure)
Strut Fork to Lower Control Arm Shear Bolt: 32 F#

Torque Specs taken from Haynes 42023 "Honda Civic 1984 thru 1991 *All models*

EDIT: Check all your suspension parts while you're in there, such as bushings, ball joints, and tie rod ends (I know, tie rods are steering, not suspension). If you put a new axle in, and it still clicks, it's possible that you got a bad one. If you change it a second time, and the second new one clicks, get your alignment checked. Chances are, you need new bushings or ball joints. These maintenance items can offset your suspension angles enough to cause the same sound from your axles that indicates that it's time to give in and replace them, even if they're brand new.

If you see anything that's obviously worn, or near it's service limit, just replace it. You can get entire suspension rebuild kits on eBay starting at $150, which includes all 4 ball joints, new tie rod ends. The bushings can be gotten from Energy Suspension *Or similar companies* or OEM. Get them from the dealer or the parts store, it's about the same price.

The only alignment spec that can be changed on these cars is the Toe angle. The rest is factory set and not adjustable without modifications. If the alignment technician's report shows that you're outside of specifications, and you haven't changed anything about your suspension, you definitely need to check your bushings and ball joints.

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Disclaimer: EcoModder.com and myself hold no responsibility for you following these directions and hurting yourself or your property. If you're not comfortable with doing this job yourself, or you don't have or have access to the proper tools/facilities, please don't attempt this repair. Please remember to use all necessary personal protective equipment, including eye protection and gloves.