If you are willing to drive an hour, or a bit more than an hour, here are two shops to consider: Beeline in Pacific Beach and Trueline in El Cajon.
I think Beeline does better quality work with better attention to detail, but they don't cope quite so well with aftermarket parts. They will adjust around them, but they won't attempt to service them unless you bring in the parts needed.
Trueline seems to be more comfortable with aftermarket parts. Modified trucks (lifted or lowered) seem to have always been a substantial part of their customer base. But they are not quite as detail oriented as I wish they were.
You will have to weigh your options depending on your own thresholds.
I do think it is a good idea to have a fully equipped shop set things up so you have a baseline. There are some things, like getting the axle centered, that they are better equipped to do. Once you have had it aligned you can then maintain it with a tape measure.