With the heavier gauge strings you're definitely going to want to check the intonation (which you did), adjust the truss rod, and probably adjust the pickup height... Larger strings put off much wider ranges of frequencies and on some high gain pickups like the ones that are most likely on your LTD the tone can become what guitar techs call "natural distortion". When the pickups are too close to the strings the sound is less clean. Even in the cleanest of settings it may still sound a little bit broken up and you may notice a lot of string noise as well.... With larger guage strings you also may increase string pull... which is also caused when the strings are too close to the pickups. Pickups are not much more than magnets, and since strings are made of metal they pull on the strings and if the pickups are close enough to the strings it can shorten sustain. What techs do to combat this is adjust the pickup height and find what's called the "Sweet spot". The sweet spot is the point where the string itself is not sitting in the magnetic field of the pickup but rather just outside it... This gives the optimal clean tone... Also, when you pluck the string it will vibrate in and out of the magnetic field which optimizes sustain... Too far away and sustain gets shorter and too close and sustain gets shorter... Here are the steps to find the sweet spot without having to take it to a tech...
1. Get the neccessary tools to adjust your pickup height...
2. Have your guitar and amp set to the cleanest tone you can get.
3. You're going to use the E,A, B, and e strings to test this out... there's no need to use the D and G strings because they're in the middle and they're going to be affected just like the other strings... Start at the E string and pluck it... Raise the bass side (the screw on the side of the bass strings) a few touches and keep doing that until you notice the string breaking up a bit.... Now back it off a little. Do the same for the treble side... the e and B strings. This is the optimal clean zone... The treble side will end up being a bit closer to the strings than the bass side because the strings are smaller...
4. Now you're going to look to maximize the sustain... so turn on some distortion or overdrive
5. now you're going to have to lower the strings a bit now... Just keep doing trial and error until you find the zone where you feel like you're getting the most sustain.
It may take awhile to get it right the first time but the more you do it the more you get use to it and the easier it is... Remember that if you have high output pickups the clean sound is going to sound dirty no matter how close they are... So you may want to skip that step and go straight to finding the sustain zone....
You won't get that answer at UG......... haha