I have a similar setup but using a 6600 rather than a CS to control it. I put a 360mm straight (24188/24172) between the 24994 and the buffers, which leaves enough space for the cab cars (as the pickup slider is on the non-cab end of these).

You may well find that you need two 24994s for each track end - mine has one to activate braking, then another to trip the reverser. The end result is something like this: main line/24994/24188/24172/24994/24188/24172/buffers.

Charles,

Regardless of using the CS "shuttle" mode or a PC there is inevitably some variation in the response time of the logic to react to the a sensor that has been activated. This may also vary (lengthen) if the CU is processing other commands.
I have also found that, aside from the programmed acc/dec, some locos "warm up" generally resulting in longer stopping distances - which in turn depends on the nominal running speed set.

With a PC , some logic can cater for the different speed curves of different addresses.

For most shuttle or shunting operations I concur with Matt, however I generally use a x172 as a contact track (aka cheaper 24994) followed by the x188 and buffer - so maybe a little shorter. This assumes I am entering the yard "at shunting speeds" AND with DEC disabled or minimal.

I hope the CS will offer some "permutations" in the future.
1) 2 stage slowdown - so that the main line run can be moderately high
2) pause - without reverse - for a main line halt
3) option to invoke functions
- i) disable acceleration for accurate stop
- ii) trigger sound on departure.
4) conditional logic - to (in your case) allow the 2 trains to operate automatically one at a time.