Webcon in the U.K. offer an offset inlet manifold: -
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Iirc, they used to offer a full kit including the correct 40 IDF's (or 44 IDF's if you preferred, kit ref. PF1201) but now seem to just offer the manifold and mention the problem with the throttle shafts- they do helpfully provide dimensions of their manifold so you can measure up to check it's suitability.
However, throttle shafts can be shortened or alternatively perhaps even replaced with the correct one's - they do stock lots of Weber carb parts.
So, not impossible for someone who know's what they're doing...
Re - rebuilt engines/tuned engines - one of the U.S. major parts suppliers (I supplied a list of these suppliers to someone on here some time ago) for the 124 Spiders lists Fiat T/c engines of various capacities both fully rebuilt or indeed tuned from c. $5000. From the description of the work they carry out, it seems like do a comprehensive job and iirc, they'll supply a dyno sheet for the engine. They usually require a core engine to be supplied (in advance or possibly? afterwards to get a refund of the core deposit), but given shipping costs and currency exchange rates this is really only suitable for U.S. residents.
I could probably fully rebuild an engine to standard spec. or even slightly 'hotted-up' for a fraction of this cost, but there again I'm not paying me for my time.