Just hacking the system up isn't any guarantee of success. The engineers who are proficient in the harmonics of flow dynamics designed a decent stock system, removed by some people because they like the appearance of 4 into 4 systems better. The loss of power is the price you pay for 'pretty.' Most VMax owners are into the 'go,' not as-much the 'show.' There are so-many variables about exhaust design, that haphazardly cutting up that pretty 4 into 4 will destroy the looks, make it more-susceptible to failure from rusting-out, since it's no-longer plated metal, and likely going to result in leaks, difficulty in removal/replacement, and possibly even-worse performance, since the owner knows nothing of engineering an effective system. If they did, they would have started with something that works to begin-with, like a full UFO 4-outlet system, and a proven track record of something that
adds power, instead of
killing power, like the Cobra 4 into 4.
We all "get" the OP bought a bike with a pretty-appearing dysfunctional exhaust. We also "get" that he cheerfully and very-stubbornly wants to 'fix' something that cannot be easily-fixed. If he would just source a stock exhaust, he would regain the horsepower the Cobra exhaust cost-him. Bottom-line: you cannot make a silk purse out of a sow's ear. Nothing can easily be done to fix the Cobra 4 into 4, to even get-back to a stock bike's power output,
no amount of jetting, no aftermarket air filter, no removing the air filter box top, no propellers in the intake tract, no "Fish" carbs (you have to be old to know about the Fish carbs), no Marvel Mystery Oil upper-cylinder injection system, no fiberglass cloth header wrap, nothing will 'fix' it, except to replace it.
Used exhaust systems are easily available on here, either stock or full aftermarket, I've bought and sold them.
Someone who wants more power, install this with a Morley jet kit:
https://www.ebay.com/itm/85-07-Yamaha-V-Max-Voodoo-Polished-Shorty-Full-Exhaust-System/310946372675?fits=Year%3A2007%7CModel%3AVmax+1200&epid=202979740&hash=item4865d91c43%3Ag%3AHioAAOSwqu9U91fV&_sacat=10063&_nkw=2007+vmax+exhaust&_from=R40&rt=nc&_trksid=m570.l1313