Hey, Chris.

1. Keep your JV Broker happy (either have an exclusive closed-door program that only your JV Broker will use to invite JV partners to join - or - if I do have a separate sign up page for ordinary affiliates make sure they are tracked separately from the JV Broker by opt-ing them into a different Aweber list)
I don't look at it simply as keeping a JV Broker happy ... just work in an professional, organized fashion to save yourself trouble of all kinds and derive the most out of your efforts.

2. Use an automated 2 tier commission structure - but this is not available in PayDotCom - therefore should I use 1SC linked with 2CO or something different?
Like I said ... Becky Dielman can modify the BM script to track 2 tiers ... PDC will pay the affiliates, and both you and I will have access to my second tier stats ... when the smoke clears, you can pay me separately for my services based on the aforementioned stats.

3. Have the JV_invite page ask for name, email and Aff id - if I am not using CB or PDC then I assume people have to enter a 2CO Aff id (or whatever you recommend I use) - BUT people must have already have signed up as an affiliate with 2CO of whoever beforehand so they know what their actual Aff id is.
If you're using 1SC in conjunction with 2CO, 1SC has it's own affiliate system that supports 2 tiers. No need to track by ID ... I'm using cookies just like the 1st tier.

Mike, I think it may be easier for you to simply recommend the following (since CB and PDC are probably not suitable):

1. Use xxx payment provider
2. Use xxx 2 tier affiliate program
The method I mentioned previously (autoresponder CSV shared via Google Docs, and a mutually shared CB account for the individual project to derive the sales report CSV ... compare the two reports) has worked well enough for me to take on some of the most successful CB and PDC launches of all time ... so I would never tell folks I don't support them.

I'm answering these questions in a bit of a rushed fashion ... hopefully I'll be able to focus on them with a clearer head, and on a one at a time basis ... a little later.

Best,

Mike