Your engine is better prepared than mine. I am starting with a stock engine to see how it does. Then maybe later do some of the engine mods you have.
Here's what I've done to my UT turbo unit; very mild porting, fully adjustable wastegate, custom downpipe. I'm not trying to make big boost with it, just reduce the resistance internally and make it more adjustable tuning to suit my engine (1500cc SOHC)....
My turbo porting is mild, mostly to clean things up and smooth transitions (same with the exhaust manifold). A little opening up of the wastegate track to allow quicker pressure response. Matching the ports of the turbo with the exhaust manifold and downpipe.
The wastegate is a aftermarket item that allows for changing of the internal spring (general boost range), adjust of the spring tension (fine tuning of the maximum boost), and adjustment of the rod (wastegate function). A boost control valve ("MAC valve") is also added to allow the ECU to control boost.
The standard UT downpipe is a good design, but it would not fit on my engine due to my air conditioning compressor. So I made a custom one. I tried to use the largest pipe sizes possible, make the bends as gentle as possible (and still fit the tight space), and separate the wastegate flow as much as possible.
The blow off valve is also a aftermarket item to make it easier to incorporate with the rest of my system.
The other improvements include a large intercooler, large-diameter short-length connecting pipes, big air filter, and as smooth transitions as possible.
Really these are pretty standard items to do for a stock turbo on most factory systems. Again, not trying to make big boost but just be as efficient as possible. And maybe this is not the best approach because these are fairly old technology turbos. Buying a modern aftermarket turbo would yield much better results. Honestly I started with the used turbo, decided to rebuild it for general assurance, and things kept going from there - project creep I guess. However I will say all of the changes/improvements I made did not cost much - far less than a new turbo - and limiting cost is one of the main goals for this particular project. It has been more of a learning exercise for me than anything.