About 20 years ago I wrote a detailed treatise on the effects of changing rod/stroke ratio on optimal engine design parameters. It's not in the public domain and it's too long and technical to reproduce even if I wanted to but I don't mind sharing the conclusions.
Rod ratios vary from about 1.6 up to 2.0 with a few unusual engines outside these limits. A ratio of 1.8 is generally found to be a good compromise between low and high rpm power and other factors like piston thrust forces. However a shorter ratio leads to a stronger rod, more compact block and reduced weight.
Essentially a longer rod moves towards and away from TDC slower than a short rod and towards and away from BDC faster. A theoretically infinitely long rod would have a symmetrical motion curve with equal accelerations at TDC and BDC and peak piston speed at 90 degrees ATDC. In real engines the rods accelerate away from TDC about 70% to 90% faster than they do from BDC. This also means that peak piston speed occurs much earlier than 90 degrees ATDC - usually between 74 and 77 degrees ATDC i.e. much earlier than the intake valve reaches full lift. If we analyse the effects of all this on optimal valve timing events and other factors we find the following consequences of making the rod longer.
1) Intake valve needs to open earlier
2) Intake valve needs to close earlier
3) Exhaust valve needs to open later
4) Exhaust valve needs to close later
5) Intake port volume needs to decrease
6) Exhaust port volume needs to decrease
7) Compression ratio needs to drop
1 to 4 can all be achieved in one hit just by closing up the cam lobe centreline angle.
The effects are all relatively small. We're only talking the odd degree or two in valve events, a few percent at most in port volumes and CR for normal achievable changes in rod ratio in a given engine. Even going from a low ratio such as 1.6 to a very high one like 2.0 would only affect valve events by about 3 degrees.
Finally although a longer rod should benefit high rpm power slightly it should also theoretically hurt low rpm power slightly at the same time. A balance needs to be struck considering the use of the engine.
If engine breathing is restricted, as it seems to be in your case, then a longer rod will hurt low rpm power without necessarily being able to show its normal benefits at higher rpm.
I come on here rarely these days and don't want to get sucked into further complex explanations but I hope the above helps.
As an aside the cylinder head is still always the most critical aspect of any engine's performance. Many years ago I was approached by a team running a short oval Ford Pinto 2 litre engined stock

. Single carb, stock internal bits other than any cam and compression ratio you liked and mildly ported heads. With their current big cam and the need to stay in one gear all the time the engine wouldn't pull out of the corners. They were thinking about reducing cam duration to get the low rpm power up a bit at the expense of top end. I suggested I look at their head porting first and just change one thing at a time. With some small but important changes to the ports and valve seat profiles the next time the engine went out they were getting so much wheelspin out of the corners they were able to lower the diff ratio, still grunt out of the corners and not have to scream the engine so high down the straights. I still remember the phone call telling me how it went and the astonishment in the guy's voice that changes to the head he couldn't really spot with the naked eye could alter the power curve so much and add not only add chunks of low down torque but extra top end too. Even their gas analyser was telling the same story. The hydrocarbons had always been sky high and it would never tick over and after the changes it put out only 200 ppm HC and sat ticking over like a road

on a 300 degree cam. They won the championship easily enough anyway.
It was fun being able to work "magic" like that for people but I'm retired now and those days are behind me.