There is a lot of work to get the S50 manifolds to fit in the E30, believe me
Mine are 95% finished, but after the hassle Ive had to get them finished (got messed around by the guy doing the work) and the fact Im still not happy with how the No.6 pipe turned out, Ive gone in for the group buy Ian posted above.
You are right that the No.6 pipe needs modding. It hits the bulkhead as well as the steering, but it doesnt stop there. The front section needs modding to clear the subframe/ARB and then the collectors need re-angling to fit the gap between the gearbox and tunnel.
The biggest headache is getting round the steering joint - the main reason Im not happy with my No.6 pipe after 2 or 3 attempts at it.
Using the E36 rack doesnt make it any easier either as the steering joint is about an inch closer to the block compared to with the E30 rack. It just means there is even less room to fit 6 pipes through.
There was talk about the head position being slightly different between S50 and M50/M52, but Im not sure what the outcome of that was.
Either way, I would suggest going for the group buy. It makes more sense than struggling with it yourself.