Rep Power: 0

Okay guys I have 2001 Civic Ex automatic with about 146k miles on it. I had originally planned to change my lower control arms, ball joints, stabilizer links as well as pads and rotors. I finally changed everything and ran into some trouble with the passenger side axle. I'm not sure if it popped out of place or if the CV joint is bad but whenever I go at a higher speed maybe 30-40 MPH I get a rough ride on the right side and vibrations too. Also when I turn right I hear a light grinding sound, as for when I change to reverse or drive I hear a knocking. I'm hoping I didn't ruin the transmission or grind out the splines but I need help with this.

 
Rep Power: 210

The knocking in reverse could be a bad motor mount making a metal-on metal tapping sound. On level ground: put the car and neutral, engine off, push it backwards and listen for tapping sounds. Another mount(s) test is engage the emergency brake and have a helper put their foot on the brake pedal (depress fully), put the car in drive an slowly accelerate while you stand to the side near the engine bay and see if the engine is lifting excessively. Some amount of lift is normal. Do the same procedure in reverse gear but make sure to allow some hesitation before going from drive to reverse or vice versa.

Worn out CV inner axle joint can cause vibrations and wobbling when driving. To test raise the front end of the car, put your hand directly under the inner joint (near differential) of the CV axle and move it straight up and down. Test both axles to compare.Outer CV axle joints when make full-lock turns can make a clicking/popping sound if they are worn out.
If the CV axle popped out of the differential there should be a noticeable gap between the differential and inner CV axle joint. Also, put you hand on the middle of the shaft and try pulling out and pushing in on the axle towards and away from the differential to see if their is excessive play. After testing you may want to completely remove the CV axle and inspect it's spline and the the differential's (gear) receiving splines for damage.

 
Rep Power: 0

I went to do exactly as you said about 20 mins ago and I popped open the hood to find grease all on the ground and lower engine bay. It looks like boot is busted now
The inner boot to be exact

 
Rep Power: 210

Replace with a new Honda Genuine oem (around $170) if you plan to keep the car a few years. If you go aftermarket (around $80-90) buy a "new" one only and avoid re-manufactured axles. Check prices on HondaPartsNow, Majestic or other reputable online Honda Genuine parts stores.

 
Rep Power: 0

I plan to keep it for a long time as it's my first car but I'll definitely go the Honda OEM route to keep the quality going. Any idea how long the install would take?

 
Rep Power: 224

I'd say maybe an hour if you have all the right tools and know what you're doing.

 
Rep Power: 210

This ^

OP you can rent a tool like this: for free at most parts stores. It works very well for removing a CV axle. Best to buy a CV axle shaft seal in case you need to replace the old one. That seal can possibly dry out and will have to be removed, carefully scraped out residual and replace with a new seal to prevent oil leaking from after the new CV axle is installed.

During axle installation use a light coating of grease on the clip ring and splines and work the axle in buy hand as far as you can. You probably won't be able to get the axle fully seated by hand so it's a good idea to have a rubber mallet on hand to knock on the outer joint end of shaft. Make sure the inner axle's clip ring audibly clicks when installing it into the differential for proper seating.

 
Rep Power: 0

I'll pick up the axle today and get an axle seal too and install it tomorrow since it's all rain here in NYC. I watched an install video and it doesn't seem too hard to get done. I've taken off the hub and rotors so many times that this shouldn't take long. Will I need an alignment after replacing the axle?

 
Rep Power: 210

Yep, with those other experiences you should be able to bang it out pretty quickly. No need for alignment afterwards.

 
Rep Power: 0

I installed the axle yesterday, it took about 2 hours tops but the install was very easy. I test drove it and everything. The drive is smooth as butter with no road noise, nothing. As for my old axle the inner boot was so busted even the bearings were broken!

 
Rep Power: 210

Good to hear. Nice when things go smoothly.