The bump noise is the tie-rod ends, more specifically the bolts. the threads wear from them not being properly torqued. Alot of the cars were on the TSB list for this issue. If they replaced your LCA, they should have used new bots but if they re-used the old ones that is the issue. The clicking noise from the clutch pedal... a bad throw out bearing? That is all that comes to mind.
P.S. Are those your actual seat covers in your avatar pic? I noticed that they are the ones from the prototype model, but not actual production ones.