I have used both, and I think the Blue Thunder have the edge, albeit slight. They seem to perform better at lo to mid rpm, and match the CJ heads at upper rpm. I would suggest them if you are going to build a race motor. If you are going to build a street or dual use motor, I strongly suggest using Police Interceptor heads. Even tho they are iron and heavy, they perform better on street duty because they have oe screw in studs and smaller ports with the CJ valves (2.25 intakes and 1.75 exhaust). They perform much better at lo to mid rpm and with judicious porting can match the CJ's all the way to 6000 rpm or so. If you are going to build a screamer motor, than use the Blue Thunder heads, and spend a LOT of time and money in the short block! I mean a stud girdle in particular if you use the 2 bolt block and expect to see some rpm on a regular basis. You can buy the girdles for about 100 bucks. I use the PI heads on my 535 with an SCJ 4 bolt block, and run hi 10's lo 11's in street trim on pump gas. My best run on slicks has been 9.97, but it cost me a twisted axle. I usually limit rpm to about 6800, unless really pushed, when I will go the the absolute max of 7200. To be clear, I usually only have to turn about 6000 or so to abuse the competition! On a less aggressive slick I have run lo 10's. And my motor isn't all that wild! Roller cam, roller rockers with the typical machining duties. I enjoy the daily driver aspect, while still being able to shut down competitors and the local tracks, and drive home while they trailer! If you get a set of early 429 heads, they have the screw in studs and can be machined to CJ valve size, thus making your own PI head! Just clean up the exhaust ports, and go racing!
