I think that you're making some assumptions that are leading you to wrong conclusions. In my opinion you have some overly strong assumptions about what is a IIC+, what is a red stripe and what is blue stripe.
I don't think that anyone with authroity (ie, anyone from Mesa who's old enough to actually know...or boogiebabies, if he's lurking here, he would know) claims that the red stripe pre-amp is the pre-amp from the IIC+. I also don't think that anyone with authority claims that the blue strip power-amp is the power-amp from the IIC+. Finally, implicit in your questions, is the assumption that this is a single design for the IIC+. Sure, these assumptions are stated on the web occasionally, but there's lots of not-quite-right information out there. Let's discuss them a bit...and let's start with the last...
A Single IIC+ Design: This is definitely false. Your question regarding the Mark III C27 cap is a good example. The equivalent cap in the IIC+ can be either a 10pF or a 20pF. It depends upon which model you have. I believe that most of the Simul-Class amps have the 20 and that many of the non-Simul-Class amps have the 10pF. IMHO, though, that has only a small impact on the sound compared to the other changes. A variation in IIC+ design which has a bigger impact on the sound is the simul vs non-simul class power amp. Also, inside the amps, the IIC+'s all have a wide variation in the type (composition) of the capacitors used throughout. This can have a moderate impact on the tone, too (some say that they have a large impact on tone). The guys at Mesa were always trying to improve the tone...or trying to compensate for changes in tone resulting from other component changes. Some IIC+'s include a 100K resistor heading into the Treble pot, while some don't (this one is also a very small difference, IMO). Some IIC+'s have the 105 power transformer and some have the earlier one. That makes a difference. Finally, many IIC+'s have gone back to the factory at some point in their life for a maintenance overhaul. Power tube rewiring (pentode vs triode), for example, is is not an uncommon mod performed by Mike B during these overhauls. So, just based on this list alone, be careful when your trying to mod your amp to be like a IIC+. Which IIC+ are you aiming for? There's no single standard.
Red Stripe is a IIC+ Pre-amp: This one is "conventional wisdom" that I had heard before. On your specific question of 500pF vs 1000pF, the answer is that most (all?) IIC+'s have a 1000pF cap at the location that you are talking about. I don't know what's in the red stripe. Furthermore, the red stripe does not "have" the IIC+ pre-amp...mostly because it is not a IIC+. Sure, maybe it has (or can be modded to have) all the same component values as someone's IIC+, but this does not make it a IIC+. The problem is that the Mark III has a Mark III circuit board and IIC+ has a IIC+ circuit board (or an modded IIC circuit board...there's another difference between various IIC+'s). The Mark III board is built using a different process (the IIC+ circuit board was built in a very old-fashioned style compared to the III). One key difference is that traces on the two circuit boards have fairly different routes. In a high-gain circuit, this matters...and it's definitely an art and not a science. I've built my own amps and, even if the schematic is the same, if I route the wires differently, the high-gain sounds different. It's effect on tone is not the size of the difference between a Mesa and a Marshall, but it can certainly be equivalent to the size of difference between the 500pF and a 1000pF cap that we've all been discussing. The Mark III also uses different types of capacitors (and probably resistors) as the IIC+ (simply because there is no one IIC+ choice), and this matters somewhat. So, IMHO, the red stripe might (or might not) have the same pre-amp schematic (ie, the same values for the caps and resistors) but it is not a IIC+ pre-amp because its circuit board is different, its circuit traces are routed differently, and its circuit elements are of different compositions.
Blue Stripe is a IIC+ Power-Amp: Similar arguments as used above for the pre-amp...circuit-board, traces, component compositions. A Mark III can never "be" a IIC+ because of these differences. The schematic can be the same, but the physical circuit will be different because it was physically built in a different way. Also, and even more important, is that the output transformer is different in most mark III's compared to most mark IIC+'s. Transformers matter...especially at higher volumes. The power transformers are different, too, and that can have a big impact at high volumes as well.
So, with all of this discussion, please keep in mind the assumptions that are in your questions. Please remember that there is no single IIC+ design to match. Also, the red stripe preamp is not (and cannot be) the IIC+ pre-amp. Finally, the blue strip power-amp is not (and cannot be) the IIC+ power-amp.
If you goal is to make changes to your amp to be more like a IIC+ by changing the values of the capacitors and resistors...well, that is a really fun process. It's extremely educational and will make you appreciate your amp (whatever brand or model) in a whole new way. Have fun, man! But, please keep it in perspective. The values of the capacitors and resistors is a very important factor of an amp's tone, but it is not the only factor. There are lots of factors that are not captured by the schematic.
Good luck and have fun!
Chip
(PS, since you sat through my long diatribe, I'll try to answer your questions directly...most Mark IIC+'s have the 1000pF. This matters for the lead channel but has no effect at all on the clean channel. Also, for your other question, most Simul-Class Mark IIC+ have the 20pF cap. The non-simul-class amps tend to have the 10pF cap. This cap affects the clean channel more than the lead. On a Mark III, which has the 2nd rhythm channel, this cap will affect that channel as well).