The issue is in the ports. It CAN be done, but when you put the intake on it doesn't run very well. ..........
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When you say it doesn't run very well, I suppose it depends on your expectations. I have been running a 409 truck engine with small port heads with big port 2 x 4 intake for more than three years and it has been OK for my use. Sure it may make a little more horsepower at higher rpm with a small port intake that matches the heads, but for just crusin' around you won't notice any difference in performance (my experience).
I am going to replace the truck engine with the Ronnie Russell built 409 stroker. The truck engine gave me quite a few fun miles as well as three trips to Thompson and back home, so I am going to give it a rest.
The T-Bird should be on it's way to Hill's Thunderbird in Ohio (to repair the damage done by the Frito-Lay truck) less the truck engine and the 700R4 transmission. Grandson and the guys at Southside City Speed Shop in St. Louis pulled the engine & transmission and I brought them home yesterday.
The Ronnie built stroker will be the fourth 409 that has been in the T-Bird. 409 #1 was the stock engine from my 62 SS Impala. 409 #2 was an engine bored .030 and with a better cam. 409 #3 was the truck engine. Looking forward to driving with engine #4 with the 700R4 and the 4.30 posi gears.