Just my .02c, k?
We've covered the "mods vs. warranty" topic quite a bit, and I hope I do not open the discussion more. All I wish to do, is add some thought to the good advice already offered above. I suggest that you debate these issues before deciding to mod, and again over what mods to accomplish. There is some risk with mods, but it's not as risky as you may imagine.
Consider first, a "sudden failure" of a major system, such as fuel, or electrical. She's dead on the pavement and it's time to call the flat bed. No chance to undo anything now, eh?
Be prepared to back your decision to mod with logical argument and proof of quality install. Be ready to negotiate, and calmly too. It's not the dealer's money at stake, it's LMs. The dealer wants your business and he shouldn't really care who pays the bill, as long as it gets paid in his shop. If it's something major, and your mods are in question, you may have to agree to some sharing of responsibility. Best to nurture a friendly relationship with your SM, get him to like seeing you drive in. When a waitress does a good job, she gets a good tip, why not the SM? If ever necessary, he may come to negotiate on your side, or, even come to ignore the special aspects of your MM.
Consider second, what's the reason for a visit to the dealer, and how does undoing mods affect that? Pulling the chip is easy, but you're not going to pull a gear, or, a torque converter, eh? Likewise the pulleys, the only mod visible to the naked eye. When you pull the chip without pulling the stat and plugs, the car will run OEM, and I don't see a problem from colder plugs and stat for the short term. But, if a road test is required, speed error may be detected, and you're back to square one anyway. Besides, things electrical last the longest when handled as little as possible. I think the risk of leaving the chip in to get your sub-woofer checked, is as risky as frying it with a static discharge while pulling it.
When you consider all the complications possible, pulling the chip may only work against you. I've been reassured by my SM, that Reinhart's chip is transparent to LM diagnostics. No one will know it's there without crawling under the dash and looking at the ECM. So, when I visit the dealer, I leave the chip in place, turned on, and let the wrench evaluate my complaint under the same conditions I discovered it. May be better to keep quiet, until it's necessary to discuss the problem at hand, and the cure.
You're not going to void the whole warranty on the whole car with a few bolt on mods, but you risk coverage on specific items. My SM told me that once I install the 4:10s, he could rebuild my rear end (if necessary), but only restore the OEM 3:55s. Of course, no two dealers are alike, and this is where you roll dice.
The suggested mods are safe to the overall car, and produce remarkable performance improvements. There has been real time field testing of these mods under a variety of conditions by many of us here, and without a hitch or side affect. Most mods can be argued to also improve emissions and reduce fuel consumption, and what's wrong with that? If the mods are what you want, you have to be willing to take risks. If you need to rely on a full 3/36 bumper to bumper warranty, plan carefully...IMHO.