I had issues getting mine into first and reverse 60k miles ago with the stock shifter and fluid. I haven't had an issue in the last 4 years and 60k miles after swapping to a Barton and Mobil ATF.
I don't know what shifter you are running, but they are not all created equal. Check your linkage for anything loose as well.
2007 Mustang GT 5-speed 3.31 gears, Hidden Hitch Receiver, Barton Short Throw, JBA LTs, Borla Touring Axle Back, and Lito tuned SCT X4. BMR SP009, KYB Shocks & Struts, J&M CC plates, J&M LCAs. 4 Piston Brembos
255/45ZR18 front 295/40ZR18 rear
Department of Boost GT450 with 2011 GT500 M122, TB, & CAI | 13/14 GT500 HE & IWP | GT500 dual pumps | FRPP 52lb | CMS Stage 2 Blower Cams | Comp Springs & Retainers | AEM boost & wideband | 8 rib conversion | Track Spec GT500 Vents