Hi,
As I understand it as a Kronos Newbie, Send 1 goes to MFX1 and Send 2 goes to MFX 2. You don't control the send level to an IFX, it is inserted directly into the signal chain (hence its name

) but you can control the wet/dry mix within the effect, and set the input gain to the effect.
When you say the sends for Timbre are greyed out, do you mean the parameters on the bottom 2 rows of the ROUTING 1 tab in P8:Insert Effect if you set ? (e.g. 8-1 on P488 of the Parameter Guide).
If so, then that makes sense if you have routed the timbre to an IFX. Page 490 explains this and that you then control the send level to the MFX from the send levels on the relevant IFX output see 8-5 on Page 492 of the parameter guide to the MFXs.
If you chain insert effects, then only the last insert effect in the chain can be sent to the MFXs, which also makes sense to me.
In general, it looks pages P488-500 of the parameter guide explains the effects structure pretty well, so essential reading if you have not been over it yet. The guides are pretty dry reading but they seem to explain things clearly as reference guides. Now I am having to program the Kronos for some gigs, I am learning so much more about it!
OT: I am getting more impressed with the Kronos as I have spent a lot of time programming AL1 and organ sounds (both tweaking existing sounds and starting from scratch) this week to replicate sounds I already have in my existing rig (spread across a Nord G2, a Motif Rack ES (with PLG150-AN) and a PC hosting sampled effects and the NI B4II Hammond clone. The Kronos is living up to my aim of replacing all of those so I can take less out on gigs. The sounds I am getting are equal (maybe different in character but no better/worse) to or better than what those units are replacing provide.