Looking to purchase a used Sig 229 with E2 grips and an SRT trigger, however I know Sig has gone through many different phases of models and manufacturing quality, can anyone suggest what time period of firearm I should be looking for ?

With used pistols, you're limited to what happens to be up for sale, so don't try to find one exactly matching what you want.  You can put the E2 grips and SRT on any P229.  However, if I'm not mistaken, older P229s will require you also change to the newer, shorter mainspring to fit the E2 grips.

Also, make sure you know that the SRT (short reset trigger) and the short reach trigger are two different things.  The SRT are internal parts, the short reach trigger is a thinner trigger with a different geometry.  

As for production years, I'm of the belief that the "bad years" just happened to coincide with the boom in popularity of forums/boards like this one, where people that had a problem had a much wider audience.  One issue posted on four forums and then linked to on 10 others makes one issue seem like 14.  That and some legitimate issues with the early P250s and the 556 rifle made people say the sky was falling.  I'd say mid to late 2000's are the "bad years" but frankly I wouldn't hesitate to buy a P229 based on the year of production.