I had the same problem when I had std brakes 91 model. And I changed to 15/16" MC with std 91 booster (abs). The paddle was better then before and took it to Wakefield with no problem at all.
Then I changed to 22v rear calipers later gen mr2 and changed front with Nissan calipers with bigger rotors and still using the std early gen booster and took it to Wakefield again for mr2 challenge January this year and the brakes were great still with std booster. You just have to get used to the paddle feel difference.

Thanks Danti,
 Can you describe the difference in the pedal's feel and travel ?  Was your previous MC was in good condition or showing signs of wear?
Theoretically, a bigger bore means less piston/pedal travel, but needs slightly more force (leg muscles) for the same braking power as a smaller bore. Is that what you found ?
 Arguably if the extra force was still small,  then perhaps a 1" bore might also be considered, but maybe that's too9 much, a rock hard pedal that you have to push like you're having a baby.
 

Regarding the paddle feel your are right but I don't feel I have to push really hard to make it stop or may be I'm used to it. My old MC was dead so that's why I changed.
Not sure about the 1" as I never used one before.
Just make sure you put a good brake fluid.
Also it depend on where you use your car most, don't spend big money on brakes if your not going to take to the track. My car is mainly for track use so that's why I went hard on brake setup and it stops really hard now.

Thanks Danti, I think I'll go the 15/16" MC.  Is that the MC on the later SW20s ? or did you get it from another
Toyota ??

Got from later model sw20. I think 94+ if it's NA or late 92 turbo model.
Try mr2 wrecking from Melb or keep looking to n line for someone Wrecking their mr2.
I think there was one on Facebook page

Will do, thanks Danti

Ensure your 15/16 mc is for abs as the port location is different. Unless your redoing your lines when you remove your abs.

Thanks 5sgte, must remember. 

Some stuff you may not already know.
 
Early JDM boosters are a 'fat' shape. Early ADM boosters are a 'thin' shape and both have the check valve on the booster body. They used a 7/8" M/C.
 
SW20 boosters post '11/91 are 'thin' and they all look basically the same.They also don't have the check valve on the booster body.
 
After 11/91 when SW20's went to 15" wheels and larger brakes they went to a 15/16 M/C and an updated booster to match that has the vacuum check valve in the engine bay on the intake manifold, so keep that in mind if updating boosters. You can get a cheap 10 mm check valve off Ebay.
 
Also after 11/93 they updated the booster again with a more powerfull one.
If you are going for a 1" M/C, that would be the one to get otherwise the pedal may need too much pressure for good modulation.
As already mentioned, always replace an ABS M/C with an ABS M/C, and non ABS with non ABS.
I also suspect that the push rods may be different lengths, but anyway it is always a good idea to check the push rod clearance if swapping units as shown in the service manual.
 

I went from a late '90 7/8 mc to a 1" (using post 94 calipers) using the stock fat booster. It simply bolted on in my case. But yes, good practice to check clearances.

Make sure you bench bleed the master, it took me half a dozen vac bleeds to get the air out.