Tire size (circumference) will affect the odometer results. Not sure how you are calculating your MPGs. But, if you don't factor for any deviation due to tire size, the calculation will not be correct, albeit small. And, other factors are involved (leverage) which affect the results. On-line tire size comparison calculators will be helpful.
The last 6 years of my career, from tank to tank (vented and filled to the rim), I consistently got over 50 MPG with my 2000 Jetta. Granted, I never drove faster than 75 MPH and mostly 70 MPH with a good amount of secondary roads which was in the 60s MPH range. I kept a very detailed Excel Spreadsheet. Including commute and on-the-job driving, I was doing about 36k miles per year. The ALH engine was totally OE, zero mods. I ran stock size tires. Today, at about 385k miles, my son is getting about 48 MPG with that car and he certainly doesn't drive like me.
I don't think I ever had the RPMs above 4100 and that was only once or twice. Briskly going up to 3200-3600 RPMs going thru the lower gears three or four times per tank of fuel provides adequate "blow-out" characteristics to keep the Turbo functioning just fine. So, I never had a Turbo issue of any kind. No, I never attempted to be a hyper-miler, but I did drive it to achieve what it was rated.
So, I believe the OP will never achieve good MPGs with all the mods as he'll always be tempted to test them. That's not saying there's some issues that may need to sorted out......... my 2 cents!