The 40/40 prop valve won't be much good to you. If you look on the firewall at your stock prop valve, it will look kind of like a flat curved piece with all the lines running out of one side (that's a bad description but it's hard to explain, just look behind the engine for something with a lot of hardlines coming out of it). The 40/40 valve looks more like a dogbone. You could use the 40/40 but you'd have to rebend a lot of line. You best bet would probably be the prop valve from an '99-'00 Si Civic. That car came with a 4 wheel disk setup and should have the same physically designed prop valve.

As for the MC, with an EX Civic, your's already comes stock with a 15/16" MC (at least my '98 EX has one). Most of the lower model Civic, which have smaller front disks and smaller rear drums have a 13/16" MC. With my '92 CX's 13/16" (which also had ~150k miles on it), it didn't push enough pressure to safelyl work with an Integra front disk setup (the Integra front setup is basically the same as an EX's). The pedal was almost to the floor before the brakes really started to bite (and I bleed the crap out of it, there was no air). I converted my CX to a 1" Integra ABS MC from an Integra GS-R but it wasn't a bolt in affair as I had to cut, rebend and reflare one of the lines because that year GS-R MC used a different sized fitting (I looked at someone's late model, 98-99 I'm guessing, GS-R and it has the same style fittings as a Civic, I don't know exactly what years are what though). The 15/16" MC is the same size as an non-ABS Integra uses with a 4 wheel disk setup though so it's more than sufficent and I probably wouldn't change it. If I had to do my hybrid's setup again, I probably would have just used and EX's 15/16" MC and saved the trouble.