So here, with the aid of a diagram, I'll show you how to calculate the size of both machine screw and interscrew bush required for your application.
Scope
The scope of fastening will cover the following;
Inner ring - typically a 20mm x 1/8" (~3.2mm) flat bar bent to shape and drilled to take the 6.7mm diameter (6.6mm drill) interscrew bush. This is the inside element of the clamping arrangement.
Coachroof/GRP - the hull against which the window is being clamped. Note that we are talking boats here (not BMW's) and so this may well vary. Checking this won't be time wasted...
Outer seal - the bedding part. This could be bedding compound ('goo'), GZ tape, or both. This should end up at 1mm thick, but may well start (ie 10 x 3mm GZ tape) at 3mm.
Outer frame flange - the part which sits proud of the hull and through which the machine screws will pass. On the new frames we have made this is ~2.8mm thick, but yours may vary, so measure it with a Vernier.
Considerations
Other points to note, before we start the numbers;
For the common raised head countersunk (RCSK) machine screws, the length is as shown below, from the end of the threaded part to the widest part of the head, which should be flush with the outer face of the frame flange.
The Interscrew bushes are threaded to approximately 1mm less than their actual length. So the 6mm bush has a threaded element 5mm long (ie it can accommodate ~5mm of machine screw within its length).
You should work on needing a minimum of 2mm of machine screw thread within the interscrew when you start to tighten up.
When the window is squeezed up leaving the 1mm of bedding, there needs to be space within the bush thread (ie the machine screw can't hit the end of the threaded bush).
The diagram
Example 1 (Easy)
Inner ring = 3.2mm, Outer frame = 2.8mm, GRP = 8mm, Scope = 3.2 + 2.8 + 8 = 14mm, plus the bedding. We're using the 9.5mm bush and GZ tape (10 x 3mm).
The end of the bush to the outer face of the frame when uncompressed will be 14 + 3 (GZ) - 9.5 = 8.5mm. Adding a minimum threading of 2mm gives a minimum machine screw length of 8.5 + 2 = 10.5mm. The nearest actual size is 12mm, giving an actual penetration of 2 + (12-10.5) = 3.5mm. When the bedding is fully compressed (to 1mm thick) this will add another 3-1 = 2mm to the penetration, ie 5.5mm. This can easily be accommodated by the ~8.5mm internal threading of the bush.
So the choice would be 12mm RCSK machine screws.
Example 2 (Harder)
As above, but the GRP is 5mm thick.
The obvious issue here is that the end of the 9.5mm bush will be proud to the outside of the GRP by 9.5 - 3.2 - 5 = 1.3mm! So the solution is either to pad out the inner ring (ie between the inner ring surface and the inner face of the GRP) or use the 6mm bush. Going through the same calculation.
Scope = 3.2 + 5 + 2.8 = 11mm. Bush end to outer frame face = 11 + 3 - 6 = 8mm. Min machine screw length = 8mm + 2mm (initial threading) = 10mm, which as luck would have it is a standard length. When the bedding is compressed by a further 2mm, this means the threaded length used in the bush is 2mm + 2mm = 4mm, which is under the maximum 5mm (phew).
So the choice here would be 10mm RCSK machine screws.
Screw lengths
Remember that machine screws come in standard lengths of 6, 8, 10, 12, 16, 20, 25 and 25mm only. Clearly you can cut the longer ones down but this is a pain to do for one, let alone 50!