I started out with two boxes, and converted a few things. Since you do not need another Thrallmaster and its model is so specific, it is hard to convert. I actually sold mine online. I never see myself using a second Luminate, so I converted my second one into another Mindbound with Double Sword by cutting the edges off the Luminate Blade and gluing some sword blades in its place. Turned out great.
As far as converting pieces go, two boxes will give you everything you will ever need to play with. I wouldn't worry about crafting too many new things unless you are going for a specific theme.
My favorite 1K list is: Thrallmaster, Luminate, Mirrorblade/Glaive x2, Mirrorblade/Swords x2, Mindbound/Swords x2 for 1K even. This is a very balanced list and has a lot of damage output. The Mindbounds are literally fodder to tie up big guys for a turn. I use the Mirrors/Sw as "Recall Bombs" where you drop them right beside an opponent who has finished activating, use a double to bump them up to 6A with "Onslaught" and shred your opponent to smithereens with 12As total. Its nazzzzteee. I have yet to fail killing a mid-range or weaker opposing character in one turn with that combo.
I use my Glaives more as "kites" instead of bombs. I try to position them in such a way that they can do some combination of Attack/Disengage or Disengage/Attack - optimally drawing them into the TM or Mirror/Sw models.
What is everyone's favorite ally choice with Cyphers? In larger games, mine is the Myrmidon, in 1K games it's the Bray Shaman.
In larger games, the Myrmidon is just an absolute beast, and fits us very nicely. He is fast, he has reach, high toughness/wounds, awesome Damage output and that base size allows you to tie up several people at once! I don't even worry about his abilities as I just "Onslaught" with him most the time. You will rarely use them, except for the occasional "Berserk". He's just an awesome block of stats for his points for Cyphers.
Bray Shaman offers so much board control for this list, he will just flat-out win games for you. A Double for his "Devolve" ability has so much utility in a warband like ours that relies on movement shenanigans, he will never cease to amaze you with what he manages to accomplish. He is also a great tie up piece for their fodder units at T4 and 25W so I am never afraid to run him up just to keep them at bay.