The T56 Magnum and TKO500/600 are worlds apart with shifting smoothness. The Magnum has a nice .80 5th gear which still pulls strong and .62 6th. TKO has a big drop off from 4th to 5th if you care when selecting the .63 ratio.
In the end the difference is about $800 and 40-50lbs in weight when going T56 Magnum. I run one in my car (RX-7) and the Chevelle is getting one as well. I've driven T5's (standard and World Class.... both are fragile), TKO's (strong but notchy), standard and rebuilt T56's, and the new Magnum. If you splurge the Magnum is without a doubt a clean sheet revision from older style transmissions and you will have no complaints if you go that path (aside from your wallet).
An '03-04 Cobra T56 could be swapped in... but in the end it still won't shift like a Magnum and it'll be a hassle doing the parts collection/calling/shipping etc assuming it is a good working trans. They have a 10 spline input shaft and it is not uncommon to shear them off in high HP setups (Supercharged Cobras).
TKO is 10 spline input shaft. T56 Magnum is 26 spline. That means your clutch needs to match up to the spline count.
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Project: 1969 Chevelle, alum 5.3, GTS76 turbo, Chiseled Perf A/W intercooler, Holley Dominator EFI, Davis TC, JRi coilovers, 14" brakes, T56 Magnum. CTS-V Recaro seats!
Coffey Fabrication Nashville, TN doing the fabwork! 800rwhp+/25mpg+/9's@150mph goal 
https://lateral-g.net/forums/showthread.php4?t=52976
1993 Mazda FD RX-7, built LS7, T56 Magnum, Holley HP, Davis Tech TC, 8.8" 3.73 Cobra IRS diff, DSS axles, Ohlins coilovers, big brakes.
CCW 18x11 front 315/30/18's and 18x12.5 rear on 335/30/18 RA1's, 2850lbs
10.31@137mph 165mph Shift-Sector 1/2 mile speed
441ci AllPro headed motor and 200lb weigh reduction in the works....
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