The 90 doesn't have the intercooler - why not break in just after the MAF, right at the front, as it's better access?
There seem to be arguments about the BB in the pipe and a blanking plate in the EGR pipe is a favoured solution, however, access there is lousy. I'd suggest suck it and see, as long as the BB is removable.
No, the series wasn't EOBD compatible till '04. However a fault indicated by the EML will self-clear after a certain number of start/stop cycles if the cause is corrected.