The problem you are describing of not making as much boost in the lower gears is quite common. As there is not much load on the engine and its not making that much exhaust gases to spool the turbo up.
In my experience most turbo cars generate a higher boost level with every gear you go up! as the load becomes greater.
What you must remenber is that the GT35R is a Ball bearing turbo (which spool up much faster than a plain bearing as in your old T3.
I would still go for a GT35R (its a very common turbo for your application) but maybe go with the smallest ex housing of .64 (i think).
I would not go smaller than you have already have.
If your problem is as bad as you say, you should start looking at the system you are running to supply signal to your wastegate.
One thing that you can do is to attach a canister (like a empty aerisol can with a fitting screwed into the end where the spray button goes) "T" it into the signal line that goes from your manifold to the wastegate. This will in effect let the wastegate stayed closed that little bit longer while boost builds rapidly and essentially "overshoots" your normal wastegate pressure, before settling back down to normal presure after a split second or two (this lenght of time of Boost spike can be tuned by the size of the canister) Ie. Bigger = longer, Smaller = Shorter.
This little trick essentially fools the system into building boost faster and harder. Also quite useful on the Highway, when you punch the accelerater, gives you a short over boost spike, to get you up and going and then it automatically drops to normal level after a few seconds.
Simple but effective, Give it a go and see what happens.