Noting that this post is from last month, by now you may have fixed the problem. If not, the easier solution is probably to remove the spacers under the carb even though I understand the reason for them is to lengthen the inlet tract, presumably for more power, I would have done the same on my recent rebuild if there were enough space to use them. I had a similar problem as I have I 1/2" SU's on a L/H drive car. In my case I chose to use a Manifold steel inlet manifold along with their latest exhaust headers and exhaust system. (Had the inlet and exhaust ceramic coated) previously I had no clearance problem with the aluminum intake manifold but when I changed it to the steel one I found out it was a bit longer, just enough so the float bowl next to the brake master cylinder would hit the base/foot of the brake cylinder. The solution for me was to file down the base of the master cylinder to give clearance.
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I also noticed you have the same Swiftune ram pipes as mine. Of course you have or will get comments about using open ram pipes. On mine I chose to use Pipercross filters. Easily removed for car meets and the like..
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"You're not a true petrolhead if you've never owned a mini" - James May 2012 Top Gear
Love the old blueprint, I can relate as a draftsman by trade, as back in the day when such drawings were made on paper or vellum using pen and ink, decades before software driven drawing applications. When I ran into my clearance problem I very briefly considered the H4 setup available from Swiftune as a possible solution but not knowing if it would rectify the situation, or make it worse, abandoned the idea straight away. Having a price tag similar to that of a ported 12G940 head was another reason but must say a lovely bit of kit, nonetheless..
"You're not a true petrolhead if you've never owned a mini" - James May 2012 Top Gear
Some good input and suggestions guys as I will potentially have the same issue, LHD with pair of HS4's. My engine currently has an HIF44 fitted with no clearance issues. Going for a more period appearance though.