Only runs 40 Degrees advanced

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I am not a fan of MSD , never have been . My suggestion: get a piston stop , find true TDC , compare that to the timing marks on the engine . R&R the dizzy with a factory unit . Set it up #1 TDC , fire the sucker up, warm it up, adjust advance to factory . If factory adjustments don't work , it's not the MSD. If factory adjustments work with a factory dizzy, use the MSD as target practice . IMO you have too many things going on that affect your engine . Too many computors running your car. If the factory dizzy doesn't work there is a mechanical issue . You can solve this . Take a step by step approach , one thing at a time . I know you have done it several times already but you missed something .
I did try putting a stock distributor in yesterday but that meant an old set of wires that I was not confident in. Because of course they’re not HEI like all the Holley and MSD caps are. I could turn it and get spark but when I put it in the car it didn’t spark so I yank that I am setting up top dead center and putting the MSD back in for another try. One guy said to pay attention to the reluctor and the pick up coil so I am going to try to set that at 13° If it would fire then I’m sure it should run. Somebody said post pictures but I don’t know what of that would help.