if you have air in thge pps then this is exactly when you will hear the groaning. and yeah, dont change the starter yet, its a really complicated and expensive procedure, so when it dies you just tow ur car and fix it. but it might take another year or 2 for it to die, you might not have the car in a year or 2, on the other hand it might die tomorrow, with those things u never know when its gonna hit ya.
about the shocks: i remember there is been an issue with an early LS models, if you search the forums you might be able to find it, i didnt find it but i do remember it was discussed here 2-3 month ago.
the vibrations might be either from the bad wheel balance or a bent rim. i had this problem and changin the rim and doing balance on the both sides of all wheels fixed the problem.
strange engine revs might be sympthoms of the dying transmission. it might be that your torque converter is not releasing but i'm not a big expert on the trannies.
whats the idle rpm when u feel the rumbling and shaking ? when ur turn on the AC ur rpm goes higher to compensate the load on the engine so just take a look at the rpm and try to increase it withthe bedal just by a little. if it will go away then i still think it might be your mount or just the car body catching resonanse. this is a 13 year old car and i really know a way to fix this.:)
oh and you do have to bleed the system every time you are doing work on it. alwys bvleed the brake system and pps system to ger tid of all the bubbles (changin brake pads is the exception)