Yeah they definitely go AFTER the SAFC. You only want to stop the ECU from seeing more than 4.3v on the map signal wire. You don't want to mess with the signal going into the SAFC.
The whole problem behind using diodes is that the ecu thinks you're running 14.5psi of boost from the time you hit 14.5psi all the way till whatever your real max boost is (lets just say 20 psi for this example). So to keep from running lean and blowing it up you need to tune at WOT @20psi with the SAFC to make sure you add enough fuel back in to not run lean, but the downside then is that at 14.5psi you will be running very rich and then it will slowly taper back to correct AFR when you near 20psi. That's not even close to ideal. The other downside is that you will be running the same timing from 14.5 to 20psi which is not usually a good idea. You might get knock, which will cause the ECU to retard the timing and will kill your power. So that defeats the whole point of raising the boost. You might also get BAD knock, which will just leave you with a blown engine. You also need to be careful you don't run out of fuel since you're running more boost without upgrading the injectors. So, in summary, not good.
The bigger fuel injector method is the safest way to run higher than boost cut on a stock ECU. Don't try upgrading the map sensor on a stock ECU, it's pointless because the fuel injectors can't handle providing all the extra fuel anyway. Just upgrade the injectors. 550's will raise the 1JZ boost cut to about 19psi after you tune them with the SAFC. 440's will give you about 17psi capability. You want to get a calculator and figure out how many percent larger the new injectors are than the stock ones, then stick that number (as a negative correction percentage) in the lo map and in the hi map. Then fine tune the hi map at WOT with a wideband and you're set. There's also vF tuning for the lo map, but that's another thing... you can search for that on here if you want, it's been covered 100 times.