Might sound obvious but if you just grabbed from the HELPS aisle the bolt needs to be same length as existing. Outside of what's already suggested, I do know that one time I used a large C-clamp to get that last 1/2" to connect up on the second side. My first guess for clunking when braking would not be endlinks. You mentioned future frontend rebuild, but outside of egged out UCA frame hole keep eyes peeled for something other than suspension that is failing - and potentially dangerous.
\'96SS SOB: SSRI, Herter Tune, Tri-Y II, , 3000 Edge, F/HO bars, METCO extendeds with CV MMC, Bilsteins, currently Vredestein Ultrac Sessanta (315/35 rear). Finally, wait for it... LT-4 knock module!
\'96FWB BUW-Butt Ugly White: PCMPerformance tune, HDFA w/ swissed filter, 1/2 SLP s.s. catback with H- and Flow Super 50s, oem opti rebuilt 3 times, SS Bars, METCO LCA, Airlift 1000, Monroe SS, PowerTrax No-Slip, CTS wheels with +1 rubber. Finally, yes again... LT-4 knock module!