I understand what you are trying to achieve and you probably are like me a number freak. It does bother me for example when I closed fraud accounts that now I have a useless ID I wil never use again. But this is not only true for WHMCS. For example, lets say a bug tracker like Mantis, also creates a unique ID per each bug, even if they are on different projects. Since one bug is just one more record in a table and the ID is created by the database system not the software.
The thing is that most developers use this setting (auto increment) because it creates a unique ID on the database automatically and you need this for data consistency as everything can and will change (like username, or name), in the end the number that never changes (and should) it what identifies a unique item. And while you might use this customer identification purposes or product (I do) you need to stop worrying about the number and consider like a trow away setting. Don't completely rely on them and instead try to query the number for each customer in case it has changed (from other systems...)
If you really need to match this to the old system, the only solution I can give you is to create dummy accounts in between the users that don't match an ID. Then if you someday register an account manually use one of those positions that hold temp data. Or the other solution is not to use the ID's from WHMCS and like someone else suggested create your own custom field, you can then have a hook that calls this automatically on each new customer registered but now you are replicating what WHMCS does and you need to babysit a parallel number systems that does the same.
It all depends on how many customers you have. The logic thing I would do in your case, is just to import the customers in order and then change the ID on my other system to match this. You need to think which one is the most important one and the master. If your new ID's will be assigned from now on forward's by WHMCS (like registering new customers) then the logic here tells you that it's your other system that should take the ID from WHMCS and not the other way around.
It would be easier just to change the ID's in the other system and then start with the new numbering system on WHMCS. This is the cheap easy way instead of creating a hook or a new number format. It all of course depends on how many customers you have, but if you need to start hacking around WHMCS then why not just create a script that does the same in the other system? Just create a script or some other task that gets the new ID for each old customers in WHMCS and then updates it automatically in your other platform/software.
It's a one time job, and once finished just start using the new ID's created by WHMCS.
Do not change or try to tamper with the ID's in WHMCS because they are used in several queries and tables to get data, you will end up with many troubles and your installation will always have troubles afterwards. The unique ID is the primary key in the database and as such has to match with other tables for data consistency.