you'd be far better off running N75 control rather than a boost controller, a boost controller only controls peak boost, it has no idea what you're doing on part throttle, and as such, it'll make the car feel sh!te when trying to drive normally.
I wouldn't bother fitting the larger injectors and trying to bodge it to run, just leave the stock injectors and MAF in place for now and DO NOT let it boost at all, that judder you're hitting when it spools up is either fuel cut or a lean misfire, and it's very unsafe either way. Avoid.
Drive it off boost, don't floor it at all, take it to the mappers and have them fit the MAF and injectors when you arrive.
If you havn't got a wideband in the car, you're risking everything the instant you allow that turbo to spool up.
even 12psi on a td05 is going to be 260bhp+ easily, so well beyond the AGU injector capabilities.