The tick could be multiple things but considering you are experiencing less exhaust flow I would suspect a bad exhaust manifold gasket or a cracked exhaust manifold. This would also cause a tick.
Well sounds like you will need to at least pull the valve covers for inspection and go from there. I would check with the company you purchased the reman engine from and see about them covering diagnosing, repair or replacement before anything though you do not want to void any warranty.Thanks Furious. I'm actually getting higher exhaust flow from the side the tick is coming from. May be a coincidence I suppose. The manifolds are new and manifold back exhaust system is brand new and 100% welded. It's definitely not an exhaust tick.