Hey Azamo! Hopefully this answers your questions.
Now to clarify, these answers are subject to change, and the nature of a "cluster" is a very open ended concept. Hopefully someone will come along to write an explanation, but its up to your interpretation as of now.
How many Clusters are there? Are there an infinite amount? What happens if you reach the end?
The Backrooms themselves are infinite, as are clusters. There is no "end". At least, not any that anyone has discovered. Its not impossible proposals/tales about finding a true end to the Backrooms would exist, but it would not be recorded as a normal level page within a cluster.
Are the Clusters separated by any major differences between their Levels?
Clusters likely will not have any major differences between others. This would only inhibit creativity and expression. Although, the standards, format, and tone may shift overtime, which we will not be able to really control.
Are there different entities between the Clusters?
I cannot say for certain if each cluster will have their own set of unique entities, but probably not. My guess is that they will have many many new entities, but seeing familiar ones like skin stealers and hounds will be common.
Are the Clusters always 1000 Levels large, or do they fluctuate in size?
It is likely that each cluster will have 1000 Levels listed, but that does not mean each cluster only has those 1000. Excluding secret, sub, and negative levels, each cluster likely has millions of undiscovered or unconfirmed levels that we will never know about. However, assuming the M.E.G. catalogs a little over a thousand, they would probably only include the ones that are most reliable to get to, and/or the most stable ones.
How are we going to tackle multiple Clusters once we fill out Cluster I?
When Cluster I is eventually filled out, we will host a contest that will determine who gets to write Level 1000, then 1002, then 1003, etc. Then, the rest of the Levels will be filled out as normal. They will probably be very different then the ones from Cluster I however, as time goes on the ideas of what is scary and creepy, and the ideas of what people want out of the Backrooms, will change.