With all due respect, We're WAY ahead of you dino

The posted runs were already using accurate numbers. It's a measure of the respect I have for you, that your post had me scrambling around to triple check everything.
To set the record straight, I measured down the centerline, several times for each port and runner using copper wire to try and mimic the profile as closely as I possibly could.
Intake runner lengths are:
HO log: 8"
Renix Log: 7.5"
99+ equal runner 11.5"
As you can see the 99+ has much longer runners meant to tune for more low torque. It's a testament to the excellent smooth flowing design versus the awful squared intake that it picks up any horse power at all. This smoother flow is quantified by comparing the port flow on my bench, to the port flow with either intake manifold attached... The difference in flow is used to calculate a flow coefficient that tells EAP how good or bad the manifold is.
The intake port is certainly not the same centerline as the exhaust, as you can plainly see the intake has a significantly higher roof than any HO head exhaust port. So the centerline couldn't possibly be identical unless the valve seats weren't the same.
intake is very close to 3 and 15/16th's, so I called it 3.9+ because the valve guide boss takes up a tiny bit of space that the measuring wire needs to occupy to mimic the port shape correctly, I am fairly confident that the port actually is designed to be 4" and the short fraction is my inability to measure the profile exactly.
The exhaust ports are closer to 3.75 than 3.5 but I sided with 3.5 in my early runs, and have since changed to 3.75 (again the guide boss).
I had derived the same plenum volumes give or take a few cubic centimeters (actually they may be identical I'd have to look) but thanks for confirming them...
I also found no significant cross sectional difference between intakes at the head port, using inside guages and a micrometer. The 99+ seems to have an intentional taper toward the plenum, but it's bloody hard to measure, I put it at 1* but it might be closer to 2*.