Every script has kinks. That's just something we have to accept as writers. Evey draft we turn in (to our writers groups, to agents, to producers, to studios) will have some shortcoming or issue. Those issues can (and will) be resolved. While we should all strive for perfection, I think that it's important to realize that perfection isn't probably. This will help more down the line than in the immediate. (This also doesn't mean that you should settle for writing a crappy script.) I'll explain.
First drafts are bound to be rocky. It goes without saying that your plot is liable to change, your characters will develop (or disappear), and the story will smooth itself out. The whole point of that first draft is to lay the foundation and realize what else you need and what you can scrap. Later down the line, though, if your scripts has taken that next step to getting produced (you've landed representation or had it optioned), you'll want to remember that it's still not perfect - at least, you will if you're like me.
With the initial excitement about attracting representation came an unwanted (though luckily short-lived) feeling of assumed untouchable quality of my spec. Someone wants to rep me and send my script out? I'm on top of the world, and the script is a killer. Come down off that high horse quickly, though, because that excitement the rep/producer shows will be quickly accompanied by notes. Lots of notes. (You already know how I had to change my intro, second act, and title.) If you want to play ball and get as much mileage out of that first big potential opportunity as possible, then accept that your script needs work. Truth be told, I'm a bit surprised by how quickly I bought into the idea that my spec needed work; then again, I had a nagging feeling that I'd get one more note that shook all the pieces into place even before I started querying.
Bottom line: be proud of your work and don't send it out until you know it's strong. At the same time, keep an open mind about changes you'll be asked to make, and just figure out a way to incorporate them in a way that suits you (or know when to fight against them). The ink dried on my option in large part because I was so upfront about my willingness to rework my script. After all, it wasn't perfect.