Theres no security issues in Layang layang. Its safer than your hotel room in KK, thats a guarantee. First of all, U need at least 2 weeks to purely enjoy the best of Layang layang, Sipadan, and Sepilok. Why?
Firsly, the amount of flying and travelling u need between these 3 places. KK to Layang layang, Layang layang back to KK, KK to Tawau, and so on. Plus, after diving, U need some no fly time, so roughly add an extra night in between diving and flying.
Secondly, the permit issue. Sipadan only issue 120 permits perday. These permits are allocated for guests at all the resorts nearby, on a round robbin basis. The longer u stay, the more probability of U getting the chance to buy the permits. Theres no guarantee of permits if U stay for only 3 days.
My suggestion is that to try to find 2 weeks. Start off from KK to Layang layang. stay there for 5 days, no more. Why? because layang layang is very very scuba oriented. no activity on offer other than scuba. and the island itself was actually only a small atoll with some sand bars. It now consists or reclaimed land with an airstrip, a navy base, and a sole dive resort. staying too long will get you boring. go diving the first 4 days and rest for the final night, as the no fly time. Then fly back to KK and continue to Tawau. From tawau take a boat 45mins to Mabul. Stay in Mabul for at least a week, minimum. Why? Because of the Sipadan permits of course. The longer U stay, the higher chance to get a permit. So if you stay for a week, U may get 2 permits. 1 permit meaning 4 dives per day. So by staying for a whole week and getting 2 permits, U can dive Sipadan for a total of 8 dives. Surely, one or more of those 8 dives will be your highlight of the trip. That leaves us with 5 remaining days. U can go diving Mabul or Kapalai or anything in between. If U plan to go to straight back to KK after Mabul, U need to allocate an extra night for the no fly time. If U plan to go to Sepilok on the other hand, U need to go to Tawau or Sampoerna, and go for a 4 hour drive up to Sepilok. Spend a day or 2 there. Then, U can continue via roads back to KK from Sepilok for 6 hours, or go back to Tawau for 4 hours before catching a flight back to KK. Spend the last couple days in KK town and remember all the epicness of Layang layang, Sipadan and Sepilok while waiting for your flight out from Sabah. cheers i hope i helped.
---------- Post added August 11th, 2014 at 07:40 AM ----------
if U wonder why it needs 2 permits to best enjoy Sipadan? well for me, if I have travelled halfway around the globe and get only a single permit, that is a poor gamble. What if your permit falls on the day of the biggest thunderstom in Sipadan? U think that U will get another permit or a refund? hehehe...or if your permit falls on the day where unfortunately all the cudas go hiding or the day that Sipadan had poor viz, or choppy seas....these are the things U need to consider. By staying longer and getting more permits, your trip would less likely to be a disappointing one. peace out.
ps-I am writing all this with assumption that by the time U arrived in Sabah, the current security issues on the East Coast will no longer be a problem. if its not, then u can make do with only one week. Just skip diving Sipadan, and spend 4 days in Layang layang, 2 days in Sepilok Reserve, and another for resting or one day for KK. cheers.