None of the issues were horrific chassis changing mods, just loads of little things, the steering column took a lot of work to get fitted correctly and I had to make a new extension shaft running through the engine bay. The rear shock mounts needed some modification to allow the coilovers to fit without sitting on a massive angle and locking up on the rose joints, the e39 wheels have a wider wheel base so they sat around an inch outside of the wheel arches, so I tried to use 3 series wheels only to find the spigots on the rear hub have a larger OD than the wheels would take, so I had to machine 0.5mm off the spigot OD. Also the steering column switches on the e39 are for a plc and won't control relays, so I had to blend together the best bits of an e36 column onto the e39 column so I could retain my steering set up but use the switches from and older 3 series!!
I am only an hour from marlin so I have been working with them to resolve most of the issues in future builds... so now they make the rear wings wider to allow for the increase in offset!