NA MX5 'Shuddering' Once Warmed Up

I bought an MX5 in December and it's been stuck in the shop ever since. It has an aftermarket ECU, Turbo and Intercooler and I'm sure other things I'm not aware of. The problem goes as follows:
When the engine gets up to temperature it revs fine until about 2-2.5k revs then shudders really badly like it's not getting enough fuel or something and refuses to go any faster. This happens both in neutral and in gear.
My mechanic says it just needs a tune probably. He already put in a coolant temp sensor, a new coil, new fluids etc etc and nothing has worked. He doesn't have the software to tune it, so will have to send it to another mechanic.
A friend that is a hobbyist mechanic said as a long shot that it might be a cracked head or head gasket (?) on the fuel side causing water to get into the fuel. Pls forgive me if any of this sounds like nonsense, I have next to no mechanical knowledge.
Just wondering if anybody thinks one of those options makes more sense or even has suggestions of a third option? I'm not exactly rich so it's hard to pick. If I tune it and it still has the same problem then I'm not sure I can afford to do the head too.
Any Suggestions greatly appreciated