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Short answer: Yes.
Long version, and not mine, rather I found it by researching your question, as I wanted to know myself.
Despite it not being our info, it might be considered being made a sticky, or I'll just stash it away if anyone needs it. Props to whom ever wrote it.
There are 3 generations of Evo Sportster heads:
1986-1990 (4 speeds)
1991-2003 (5 speeds)
2004-present (rubber mounts)
Interchangeability:
Within a given generation, the heads are mechanically interchangeable between the different models, i.e. all bolt holes line up and no needed features are missing. Valve geometry is the same: 27 degree intake & 31 degree exhaust for a 58 degree included angle, and the location of the valve tips is the same.
The rocker box bolt pattern has not changed across any of these generations; a 1986 lower rocker box will bolt right up to a 2006 head and vice-versa. The only thing you need to be aware of is that the crankcase breathing arrangement has changed at each generation. 4-speed models provided no facility in the head for a crankcase breather. 5-speed models incorporated crankcase breathers into the carb mount bolts, and use a different middle rocker box that has a check valve incorporated (aka "umbrella" valve). Rubber mount models use an air/oil separator & check valve unit bolted into the lower rocker box, and do away with the middle rocker box, using a different top cover.
91-03 heads have been successfully fitted to 86-90 models. The major difference you need to be aware of is that the spacing between the pushrod holes is different between a 4 speed and a 5 speed. This is because the cam box geometry is different and the pushrods are at a different angle. So pay attention to the potential for pushrod rub where they pass through the heads into the rocker box.
04-up heads have been successfully fitted to 91-03 models. The new heads have the right front bolt hole relocated inboard 1/4", and also use 7/16 fasteners as opposed to the 3/8 fasteners used on the 91-03 models. You can either modify your existing front mount, or more recently a new mount has become available that solves this issue. Also, be aware that the 04-up heads have larger fins and will overhang 91-03 cylinders somewhat, most noticeable on the left side. You can use your stock 91-03 rocker boxes or use the 04-up rocker boxes, either will work fine.
Any time you're putting a different set of heads on your bike, you need to be aware of the chamber size & shape and how it relates to the piston you're using, to make sure they're mechanically compatible and will give the desired compression ratio.
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HERD meber #10
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Following my instructions will likely lead to death, mental retardation and/or bodily injury, consistant with eating lead-based paint chips, and by doing so, will release me, my family and my dog from any legal action(s) for listening to anything I recommended.
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