richardp01, It is highly (!!!) unlikely that the domes collapsed from use, more likely from careless cleaning or incidental contact.
Small dimples on the speaker driver domes are often inconsequential.
The midrange surround tear can be tricky, as it is made of paper. It might be best to have it professionally repaired. I'd suggest Thiel https://www.thielaudio.com/parts-services-department/ or Miller Sound http://millersound.net/. I recommend both highly, and if it were up to me, I'd let price decide.
As for the collapsed domes, I suggest you try to find or make cardboard tubes/cones with one opening of the same size or just slightly larger than the speaker driver dome under consideration. Gently place the appropriately sized tube/cone opening over the offending opening, and your mouth over the other end, then gently suck. Don't use a vacuum cleaner as it might be too powerful and detach the voice coil.
Should you need to remove the speaker drivers, I suggest that before starting you have a small adjustable height table or step stool, a small cup, appropriate equipment for desoldering/ soldering including high quality silver solder (Thiel used to provide a small length of this, but I'm not sure if they still do) , an appropriately sized non-magnetic screwdriver, writeable tape, a marker, appropriately sized boxes and packing material for the speaker drivers.
First cut two pieces of tape into 2" lengths for each driver to be removed. Then mark one piece of tape with a "+" and the other with a "-" for each pair of tape pieces. If you don't have a non-magnetic screwdriver, proceed with care. Place the height adjustable table/step stool top right next to the height of the driver to be removed; warning the speaker driver leads might be quite short. Put the screwdriver, tape pieces and small cup on said table/stool.The speaker driver magnets are quite powerful and can attract and drag a typical screwdriver with such force that can cause speaker driver cone tears. When using a typical screwdriver, place the non-screwing hand over the speaker driver cone without pressing down, then carefully place the typical screwdriver between thumb and index finger of the non- screwing hand before removing the first screw. Remove screws from speaker drivers/ speaker baffle, then place screws in the small cup. Desolder one lead from the back of the speaker driver, then place speaker driver on table/stool. On the back of the speaker driver there will probably be a marking denoting "+" or "-"; place the previously appropriately marked "+" or "-" piece of tape on the speaker lead that has just been removed. Repeat with the other speaker lead and put the other appropriately and obviously differently marked piece of tape on the other lead. Repeat as necessary. This will be quite helpful when it comes time to reinstall the speaker drivers.
The 3.5's midrange drivers have a reputation for requiring "maintenance". Though they would appear to be of generic origin, Jim Thiel had these otherwise off the shelf drivers customized for his use in this particular line of speakers. The 3.5's haven't been made in decades. Should you replace any of them, you might want to keep any them around, no matter how damaged they appear for potential "rebuilds" should the need arise.
Though perhaps a bit more risky, yet perhaps better value laden; another approach might be to buy another 3.5(s), using the parts you need and either keeping the remaining parts for future use or parting out the remaining parts for resale. FWIW, I might be interested in some of those parts for future considerations.
Good luck, let us know how it turns out.
Small dimples on the speaker driver domes are often inconsequential.
The midrange surround tear can be tricky, as it is made of paper. It might be best to have it professionally repaired. I'd suggest Thiel https://www.thielaudio.com/parts-services-department/ or Miller Sound http://millersound.net/. I recommend both highly, and if it were up to me, I'd let price decide.
As for the collapsed domes, I suggest you try to find or make cardboard tubes/cones with one opening of the same size or just slightly larger than the speaker driver dome under consideration. Gently place the appropriately sized tube/cone opening over the offending opening, and your mouth over the other end, then gently suck. Don't use a vacuum cleaner as it might be too powerful and detach the voice coil.
Should you need to remove the speaker drivers, I suggest that before starting you have a small adjustable height table or step stool, a small cup, appropriate equipment for desoldering/ soldering including high quality silver solder (Thiel used to provide a small length of this, but I'm not sure if they still do) , an appropriately sized non-magnetic screwdriver, writeable tape, a marker, appropriately sized boxes and packing material for the speaker drivers.
First cut two pieces of tape into 2" lengths for each driver to be removed. Then mark one piece of tape with a "+" and the other with a "-" for each pair of tape pieces. If you don't have a non-magnetic screwdriver, proceed with care. Place the height adjustable table/step stool top right next to the height of the driver to be removed; warning the speaker driver leads might be quite short. Put the screwdriver, tape pieces and small cup on said table/stool.The speaker driver magnets are quite powerful and can attract and drag a typical screwdriver with such force that can cause speaker driver cone tears. When using a typical screwdriver, place the non-screwing hand over the speaker driver cone without pressing down, then carefully place the typical screwdriver between thumb and index finger of the non- screwing hand before removing the first screw. Remove screws from speaker drivers/ speaker baffle, then place screws in the small cup. Desolder one lead from the back of the speaker driver, then place speaker driver on table/stool. On the back of the speaker driver there will probably be a marking denoting "+" or "-"; place the previously appropriately marked "+" or "-" piece of tape on the speaker lead that has just been removed. Repeat with the other speaker lead and put the other appropriately and obviously differently marked piece of tape on the other lead. Repeat as necessary. This will be quite helpful when it comes time to reinstall the speaker drivers.
The 3.5's midrange drivers have a reputation for requiring "maintenance". Though they would appear to be of generic origin, Jim Thiel had these otherwise off the shelf drivers customized for his use in this particular line of speakers. The 3.5's haven't been made in decades. Should you replace any of them, you might want to keep any them around, no matter how damaged they appear for potential "rebuilds" should the need arise.
Though perhaps a bit more risky, yet perhaps better value laden; another approach might be to buy another 3.5(s), using the parts you need and either keeping the remaining parts for future use or parting out the remaining parts for resale. FWIW, I might be interested in some of those parts for future considerations.
Good luck, let us know how it turns out.