Check out Panzerfaust's solution:
This is an old issue with (in my case) a simple answer, but my theory is that you have to take action to correct the BS factory shifter issues BEFORE you make repeated grinding/clashing 1-2 upshifts which will damage the trans and compound the problem into an issue that requires warranty action. The issue (I believe) is that the factory shifter stick (NOT the factory shifter) is the culprit here. It is so over-isolated with rubber bushings that it makes experienced manual trans users look like rookies.
With over 25 years of man. trans. use under my belt, I was humiliated by clashing gears on the 1-2 upshift on my 2011 GT500. It happened to me 2-3 times (and I read about it all over the web) and I immediately went into diagnosis mode. Sitting in my car in my driveway with the engine off, I ran through the clutch/shifter motions of an aggressive 1-2 upshift repeatedly, something I'd done thousands of times in reality, with no problems.
Then I slowed down the clutch/shifter movements I make, into slow motion. Lo and behold, I could feel that as I moved the shifter handle from 1st to 2nd, when I hit the shifter stop at second, there was a secondary, almost imperceptible movement of the handle a tiny bit to the rear and I could feel an additional mechanical sensation through the handle. That sensation was the final, full engagement of 2nd gear.
Though I had, in my mind, been timing the release of the clutch by my left foot to the arrival of the shifter handle's end-of-rearward-travel into second gear, that was not the case.
The culprit was the ridiculous factory rubber-mush isolation of the shifter stick. It was NOT the body of the factory shifter proper. What my 25 years of man. trans. usage had programmed my brain to do was to release the clutch when my right hand stopped noving rearward. Because of the over-insulation of the factory shifer stick, there was a fraction-of-a-second of a delay between the shifter hitting the second gear shift stop (thus compressing the rubber isolators) and the rubber isolators on the stick having time to rebound (de-compress) and then transmit the force from the shifter stick to the shifer body and finally get the second gear shift to complete.
Sounds hoakey I know, but a fraction-of-a-second mis-timing of clutch release to gear engagement will result in a gear clash. Below is the text of my post to Team Shelby.com (post #29 on the thread at: Shelby GT500 Shifter vs. MGW - Team Shelby - Page 2 )
I simply bolted up (with NO RUBBER ISOLATION) a Hurst stick to my factory shifter and I've never had the grind since. Because I caught it early enough, there was no harm to the trans. Your mileage may vary.....
Team Shelby post now follows, pics are on that thread:
Before anybody runs out and spends hundreds of dollars on an aftermarket shifter and the labor to install it, I'd advise trying what I did. When I got my 2011 SVTPP Shelby, the shifter felt rubbery and I was having the 1-2 upshift grind problem. I was planning on getting an MGW shifter, but decided to tear down the stock set-up first to see if I could improve it for less $$$. Lo and behold, the stock stick has more rubber on it than a high school senior on prom night.
I realized I had been having the 1-2 grind because I thought the car was in second gear and had been releasing the clutch too early, while in reality the over-rubber-isolated stock shifter stick was not transmitting my force on the stick to the actual shifter arm. The trans was not fully in second gear when the clutch was released, hence the grind.
I bought a Hurst chrome stick (#7201) off eBay for $40. It came w/ 2 bolts with bushings that adapted the smaller-diameter metric bolts to the larger 3/8" bolt holes on the shifter and it also came with the rubber boot adapter. Shifter stick has 3/8" coarse thread for your choice of knob. I bought a Roush shifter boot from JEGS for ~$30 and it fit the boot adaptor like a glove. I removed the stock stick and all the rubber isolators, installed the Hurst stick (bolting it directly to the stock shifter w/ no rubber isolation), the Roush boot and a Hurst T-handle I had lying around my garage. Total install time was about 60 mins and was done entirely from the driver's seat.
Result is an expenditure of ~$75 for a shifter that works with the rock-solid feel of a bolt-action rifle. It was an unbelieveable difference over the rubber mush crap that came from the factory. It has virtually no rattle or vibration and the 1-2 grind issue is gone. It cranks off 1-2 upshifts with ease. I did re-discover the fact that the aluminum t-handle gets a bit warm in a sunny parking lot. I also have about a half-dozen shift knobs I've acquired over the years, including a vintage 1960's-era Muncie pattern knob and a Mopar-esque pistol grip, so I switch them up from time to time for some variety.
So, before you throw the baby out with the bathwater, the problem w/ the factory shifter is the rubber isolation that they install. They totally over-do it, so that there is never a complaint from somebody who buys a Shelby and complains about shifter vibration because they expect a Rolls Royce level of cabin noise......just throw out the bath water (the rubber isolation) and keep the baby. You'll save a lot of $$$$. If you don't like it, you can always subsequently buy an aftermarket shifter and re-sell the Hurst stick on eBay.......