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Andrew,
There are many opportunities for optimizing ProE and IE for PDMLink and corresponding workspace functionality. I would start with the PTC Knowledge Base for TPI 141290(which makes reference to appropriate BP documentation and some other TPI's including the IE hotfix) and the performance whitepaper.
In general, I also recommend some deployment support from PTC Global Services, particularly for ProI migrations. Plenty of customers have performed migrations on their own, but I have also seen several fail with fairly catastrophic results - best to take the safe route and mitigate risk with corporate IP. As part of the migration effort, you can make sure that PDMLink or Pro/I is configured properly and optimized for performance. A successful, performant deployment willalsohelp mitigate end-user adoption pitfalls.
As for IE versus Firefox, there is a general performance difference due to how the browser handle javascript and also handle refresh commands. Please see TPI 141283 regarding best practices (use direct urls versus "refresh" icon or F5). Firefox 3.5 is NOT supported with ProE until production Wildfire 5 and is supported as the standalone browser as of R9.1 M020. Earlier versions of Firefox are supported with PDMLink but you should refer to the platform support guide for more details.
Hope this helps!
Steve