I agree with @fitzsimmons build for Ranged Defense and use a Resist Shield of your favorite flavor. Personally, I like Mu for 'Bots because you can also get access to a small radius Immobilize that has -KB built into it (so you can lock in the most important target and keep him from being blow out of burn patches).
Make sure to add the two +Global Defense IOs into your resist shield, adds +6 DEF vs ALL for yourself, which stacks nicely with Protector Bots bubble, Maneuvers, Hover/CombatJump.
Definitely the pet IOs. You can fit 3 in there rather comfortably with the Overwhelming Force IO in the three little bots. I'd put 2 of the Pet Defense IOs in Prot Bots, since they are lower damage and trying to buff their Defense / Heals is not worth it, in my opinion. The other 4 slots can be used to get them to 84.4% To Hit, Damage with frankent-slotting.
Put one Defense IO in the Little Bots, and the other 4 slots to get them up like Prot Bots.
Eventually put the level 50 15% Resist IO into Big Bot plus a Sudden Accel. KB to KD converter for him. The other 4 slots to get him to 84.4% Acc/Dam/EndRedux.
You can up the damage on each to 9x% by swapping out frankenslotting and reducing EndRedux to 6x%, but I find for long battles I prefer more EndRedux. Its your call.
I can toss out a build for you, but it might take a few days as I'm pretty busy this weekend. Let me know.
I like the idea of Bots/Rad, and I think the pair of them will play nicely together.
Oh, don't forget a Lockdown +2MAG Hold proc in Choking Cloud. It will take care of most minions and some Lts fairly well. I use it all the time on my Ill/Rad Controller and only need to stack holds on Bosses while Choking Cloud does admirably in Lts/Minions.