A small thing first. Master Spellthief has a debated effect. If MS actually adds class levels then MS & SC don't actually stack, otherwise everything checks out.
Now onto your questions.
1) Yes, Chameleon has it's own full spell progression and is treated as an Arcane Spellcasting Class so long as you choose Arcane Focus for the day. Since it is only an Arcane Spellcasting Class while Arcane Focus is applied then you can't use it as the target of SC's spells per day leaving you to stack SC4 with Wiz5 for CL9 to all classes, Chameleon would override with it's higher CL20
Your caster level is equal to twice your class level.
Master Spellthief can then total everything giving you a CL of 56 while using Arcane Focus and 36 when not using Arcane Focus.
2) For the reason stated above I must agree the answer to this one is no. Chameleon is only an Arcane Spellcaster while under the effects of Arcane Focus.
3) All CL bonuses from items are added only to the final result of the stacked CLs. Since bonuses from the same source do not stack your Orange Ioun stone would only increase your CL by +1, not +1 per class. It will still boost all your classes by +1 but after all stackings have been completed. So your CL would be 57 using an Orange Ioun Stone with Chameleon under Arcane Focus, and 37 otherwise. (CL of 73 in the first build) +4 from Bead of Karma brings these up to 62, 42, & 77.
4)It is unclear as to how this would actually progress. I would wager that you could progress either Wizard or SC with those 9 levels of a prC and have the same result. If this result is a higher CL or no CL increase I'm not certain. It might only just add 9 to your CL even. There's several ways this could go.
- CL9 x 4 = CL36; CL36 + 9 = CL45 (prC9 only increases final CL by 9)
- CL9 + 9 = CL18; CL18 x 4 = CL72 (prC9 increases Wizard or SC by 9 then stacks)
- CL9 x 4 = CL36; CL36 + 0 = CL36 (prC9 doesn't increase Wizard or SC CL)
Any of these are possibilities... regardless of which one it is though you will still have a higher CL than normal for your level.-