Adjusting stat blocks really sucks.
I have this really nice file of 3 line (1st edition style) stat blocks for all 3e srd monsters. I just cut and paste the stat block into my notes (hurray for word processors!).
My theory of stat block adjustment is, "I'm just publishing this for my own personal use, small errors are acceptable and if it comes down to it, represent the natural variation in real world creatures."
The only hard parts of stat block adjustment are skill allocation and spell listings. HD adjustment is usually pretty quick, especially when you've done it enough that you've basically memorized the base saving throws. Skill adjustment is usually irrelevant anyway. Besides a handful of skills directly related to combat that might come up, most definately won't come up (or if they do, you can assign them then). My general theory when I want to allocate skills is to figure out how many skills the critter has, and how many points that they have and list those skills that are relevant as if points/skills evenly. As for spells, odds are the creature won't last more than 6 rounds. Listing more than six or so spells (plus some maybe some buffs) is generally gratuitious.
My theory of 'balance' is simply, "Go with your gut.", and if any 'checking' is required to see if you got the balance right, "Go with the math (simulate the combat), not with the rules." A few quick checks to see how much damage the creature is expected to do per round and how long it can stand up to the PC's is much more important than properly calculating CR according to the rules formulas.
If stat allocation did start to consume alot of my time, I'd probably create a tool (excel, C#, something) to do it for me. And, before I'd do that, I'd probably look around and discover that such a tool already exists because I can't be the first DM to think that.