Diagnosing steering/suspension issue
 

2006 CRV. We set off on the mission or replacing the lower control arms and the ball joints as the boot tore while separating it. Of course an "easy" job never goes well. Anyways, I'm assuming that we did things in the wrong order and messed up a few things along the way. We had a lot of issues trying to remove the axle nut which we still haven't gotten off yet... But I think whatever the issue is started there. (sorry this is long, hoping the explanation will help with the solution) the control arm was already removed and I'm thinking not much was supporting the system while we tried to remove the axle nut. Seems that the axle popped out a bit during this process. We ended up removing the strut, loosening the, I think, steering or suspension knuckle, caliper and rotor to pop the axle back in place. Got the lower control arm in, finally, and then basically put everything back where it was. Took it for a test drive and it felt like the wheel was wobbling a bit like you would get with loose lug nuts. They were tightened properly so I don't think it's that. There was also what I would describe as kind of a rotational clunking. The intervals were pretty consistent. So, I'm wondering where we should start looking. Does it sound like it just desperately needs an alignment, or an inner CV joint was messed up? We're doing YouTube mechanics on a budget which can unfortunately become more costly at some points. It's been raining like all hell and we really need to get the job done ASAP. Hoping someone has a suggestion of where to start looking for the problem. Thanks.

Wow, sorry to hear about your troubles. But, it sounds like you did a lot of stuff that wasn't necessary which only added to the problem.
And at this point in time, it would be best to get someone who knows the suspension system to fix what is wrong.
I can not see the vehicle and can not say what needs to be done, especially with all that has been done.
Wish you good luck

Note: Axle nut may have a cotter pin which needs to be taken out first to release the nut.
Then using the proper socket size and impact wrench, should come out easily.
Lower ball joint require a bit of experience to break it free by hitting what it is stuck in. Too hard and it can deform the knuckle. Too soft and it will not come out.
Of course there are tools that do the job quickly. Pickle fork being the one that tears the boot.

You pulled the axle out of the tranny while still in the hub?