For the tube lengths' calculations I went off two sources:
One was the work of a fellow member here a few years back. You might recall the thread where we were developing the "ideal header" (all tubular exhaust header) to make from scratch. He did a ton of research and found all the reference he could on how to calculate everything for the specific specs of the engine, desired power band, etc. Those dimensions were calculated to build the header and corresponding exhaust system.
The other source I used was a very old book by Colin Campbell, "The Sports Car Engine, Its Tuning and Modification". It's considered to be one of the original 'go-to' references for performance modifications on small engines like the X's. Funny side note, it was the first hardback book I ever bought new from a bookstore...I think I was about 7 or 8 years old (what does that say). Anyway this was written looong before the computer was even created, so it gives an entire chapter of theory and mathematical calculations on how to design an exhaust system.
Both sources focused on 4:2:1 designs, and both had very similar results (I'd have to look up the details again if you are interested). That's what I was going by when I said the stock manifold has runners that are too short for an ideal design (based on my parameters). So I'd have to go back and recalculate everything to accommodate the shorted "primary" lengths on these manifolds (haven't done that). To be honest I don't think it will make that much difference; there are other practical considerations to be taken into account, plus any given design is made to optimize performance at a specific RPM and we don't drive normal cars at one RPM constantly.
Interestingly I found that getting the desired lengths for the downpipe and exhaust (the secondary and tertiary pipes) was a lot easier than I thought it would be for a mid-engine car with little space behind it. In fact the calculated lengths are almost too short for some layout options. Therefore I choose to go above the rear-suspension cross-member. This layout was actually much easier for my design; but I'm not running a cat, I am not trying to keep anything stockish, and my car will be VERY low (very little ground clearance) and it keeps the pipes up away from the ground.
Obviously there is more room from side to side than from front to back, so the muffler needs to be mounted transverse. That means a couple 180 degree bends of the exhaust to accommodate it, and that puts a lot of length into that tertiary section.
To minimize the number of bends I choose to keep the secondary pipes stacked front-to-back (rather than twisting to side-by-side) as they travel down and through the opening above that cross-member. That allows them to bend to one side just before the final merge (2:1). However I am not adding the flex joints at the flange like you have, so that made it much easier. It is definitely preferred to have those flex joints, but this car will be more of a "track day" build. So minimal exhaust (little weight) and minimal use (little wear/tear like a road car has), plus vibration/comfort isn't a real concern.