This was happening to me with my twin setup. Pretty much the exact scenario that you described. You have a few options and I'll start them in order of least difficult to most difficult...
1. Go non-sequential!
Remove all non-essential rats nest components and manually set the flappers to open. You can do this without removing the actual turbos and it would take about a day to do if you are used to the Cosmo's engine bay. Lots of guides are available online. Basicallly, you need to make up 8, 3K Ohm resistors attached to space connectors. You plus these into the solenoid connections after removing them to avoid error codes. I can dig up more specific info for you.
2. Go Single!
I'd recommend something like a T04Z, T04R, T04E (what I have currently got) or GT35R. Borg Warner are also recommended but I haven't had any luck with these. Going single has its charms - consistent boost levels, ability to find replacement parts easily etc. The downsides are that you are opening a
can of worms. I went single for the exact same reasons and my car ended up being off the road for a year.
I refuse to go into any sort of debt because of my car so I was essentially just spending my "allowance" money each month to acquire parts. I did most of the work without the assistance of a mechanic also so that saved me $$$. The reason why I say it is a can of worms is that there are a ton of small things that you will need which quickly add up... gaskets, new studs etc. But even worse, you start to think to yourself "while I am here I may as well..." ...and that was pretty much what I did for a year.
Do I regret it? Hell no. The car is so much more fun. It's like sitting on a nuclear arsenal waiting to unleash it. With the factory turbos, sure you had a massive arsenal of power, but the launch button could not be guaranteed to work. With the single set-up you know that you can unleash the monster at will.
For the trials and tribulations of going single on a Cosmo, check out my build thread.
3. Restore the factory system
I rate this as being the most problematic of all three. Why? because stuff under the bonnet is old and going to break. You pretty much need to consider that everything involved in that system will need to be replaced with new parts. When I was working on my car connectors would just break when I touched them. I knew to be gentle but still things were extremely brittle.
This is the point at which you go to your local Mazda dealer and they will do one of two things... The first and most likely option is that they will tell you to go away and find part numbers for everything. The second thing which they will do is charge you a handsome fee for these parts. Don't get me wrong, I am not complaining about the price of these parts because it was a very expensive (and complex) car. My main issue comes back to the fact that 15 years from now, you are going to be doing the exact same thing. You'll get about eight to ten years of good drive ability, then the gremlins come back.
The other reason why I rate this as the third option is that you will more than likely need to do all of this work yourself unless you have serious disposable cash. It CAN be done though - but for time invested / money spent I think that this option has the least return on investment. Plus every time I see this picture I cringe..
I would say it comes down to your long terms plans for the car. All of these options mean that you will be committing to owning the car for a long period of time. I decided to put the time into going single because I have no intentions of selling my car.