I recently picked up a F-14 and have started going though it to bullet proof it using many of the things I learned from Vid's System 3-7 thread. Here is what I have done so far:
1) Checked all fuses in the machine to ensure they were the correct value. Everyone should do this first thing when getting any "new" machine.
2) Replace the capacitors on all the boards and playfield (sling and pop bumper switch caps). System 11 games are 25+ years old which means many of the electrolytic caps are no good any longer. GPE has all the capacitors you need for this at a great price.
3) Re-build the snubber boards (if your machine has them) under the playfield with new capacitors and 2 watt 150 ohm resistors installed raised off the boards a 1/8 inch. Re-flow remaining through hole pins on the relay and diodes.
4) Re-build the high voltage section of the power supply and reduced the voltage to 91V to preserve the displays. GPE has a complete kit of parts for a few bucks http://www.greatplainselectronics.com/proddetail.asp?prod=WAN-HVP-KIT Vid's instructions are for System 3-6 but the high voltage power supply in System 11 use the same parts. See Vid's instructions here: http://pinside.com/pinball/forum/topic/vids-guide-to-bulletproofing-williams-system-6/page/2#post-957591
5) Replace the battery pack with a 3 F capacitor (cheap ones available on eBay) to backup the memory with a capacitor instead of batteries. I like this solution over installing a remote battery holder to protect your CPU board from battery acid damage. Simply solder a couple short pieces of wire to the capacitor leads and connect the + lead on the capacitor to the lower left battery holder hole (+ sign next to it) and the - lead to the upper right - hole. Use a small piece of double sided foam tape to secure the capacitor to the CPU board. On System 11 boards, you need to either remove and install jumper in place of D2 or solder a jumper wire across it to enable charging of the capacitor. Leave the machine on for several hours to fully charge the capacitor but once it is charged, it will only take 30 minutes a month of "on" time to keep the capacitor charged.
6) Replaced the TIP 42 lamp matrix transistors with IRF9Z34 ($1 each from GPE http://www.greatplainselectronics.com/search.asp?pg=1&stext=IRF9Z34&sprice=&stype=&scat=). This reduced the temperature of the 27 ohm resistors in half (from 195 - 220 degrees to 90-100 degrees) and the transistors themselves run about 30 degrees cooler. This will eliminate quite a bit of heat from the backbox and greatly improve the longevity of components in that area. No need to replace the transistors in the other half of the lamp matrix with MOSFETs (like we do on System 3-7 boards) as Williams already updated to a more efficient design with a single TIP122 transistor that does not need wasteful bias resistors.
7) Add fuses between the transformer and bridge rectifier screwed to the backbox. See Vid's post here for instructions: http://pinside.com/pinball/forum/topic/vids-guide-to-bulletproofing-williams-system-6/page/2#post-945742
8 ) Re-flow header pins on Power Supply, relay boards, etc. Replace power supply molex pins and wire connectors especially if they show signs of getting warm (yellowing plastic, etc).
9) Replace Molex pins on boards (CPU. sound, display, etc) and Molex connectors on cables. Replace CPU-sound board and CPU-display board ribbon cables.
10) Replace flash bulb warming and current limiting resistors. Make sure to leave an air gap between the resistors and the boards as these resistors get HOT!
11) Replace CPU board resistor packs: See Wayout440's post below for more information http://pinside.com/pinball/forum/topic/williams-system-11-bullet-proofing-thread#post-1211865
Please feel free to add your bullet proofing ideas to this thread!