To start out with, you don't have shock absorbers, you have struts on your car and the average cost for 2 installed is around $400. The front end should be aligned after.

As far as the C/Vs are concerned, changing boots is not done any more. The entire axle can be replaced with a new unit for less money than it will cost to remove and disassemble the old one and the joint is likely damaged anyway from all the dirt and grit that got inside it. The average to replace an axle is $200 to $250