On the whole network there are hundreds of boxes with lever frames, some of which don't operate semaphore signals (Like the Stockport 5), or just small semaphore shunt discs (Like St Helens). Not sure what you class as "mainline" but off the top of my head I can think of the following locations:
In England:
- The Tyne Valley Line (Blaydon to Corby Gates)
- The Cumbrian Coast (Wigton to Barrow-in-Furness)
- The Furness Line (Barrow-in-Furness to Carnforth Station Junction)
- The Bentham Line (Carnforth Station Junction to Settle Junction)
- The Settle to Carlisle (Howe & Co's Sidings - Hellifield South Junction)
- Bishop Auckland Branch at Shildon
- Windermere Branch at Burnside Higher
- Barton-upon-Humber branch at Barrow Road, Oxmarsh Crossing and Goxhill
- Skegness Line (Sleaford - Skegness) excluding Thorpe Culvert, Sibsey and Sleaford East
- Cornish Main Line (Lisekard to Penzance)
- Parbold on the Wigan to Southport Line
- Midge Hall on the Preston to Ormskirk line
- Rainford Junction on the Wigan to Kirby Line
- Ellesmere Port to Helsby
- Plumly West on the Stockport to Chester route
- Horrocksford Junction on the Clitheroe Line
- St Helens on the Liverpool to Wigan Line
- Ryde St Johns on the Isle of Wight
- Bopeep Junction and Hastings
- Worcester and Droitwitch Spa
- The Cotswolds Line at Moreton in Marsh and Norton Junction
- The Malvern Line (Henwick to Hereford)
- The Derby to Stoke Line (Eggington Junction - Caverswall Crossing)
- Parts of the Scarborough to York Line
- Gristhorpe on the Hull to Scarborough line
- The Harrogate Line (Poppleton to Harrogate)
- The Whitby Branch at Nunthorpe
- The Warrington Low Level Line (Fiddlers Ferry - Arpley Junction)
- The Peak Forest Area (Great Rocks Jct & Peak Forest South)
- The Buxton Line (Buxton - Furness Vale)
- Glazebrook East on the Liverpool - Manchester Line
In Scotland:
- The Stranraer Line (Kilkerran - Stranraer)
- The Dumfries Line (Annan - Kilmarnock)
- West Highland Line at the Pass of Brader (stone signals) and Fort William Junction
- Cupar to Tay Bridge South
- Stirling to Perth
- Dundee to Aberdeen (exclusive)
- Aberdeen to Keith Junction
- Perth to Aviemore (excluding Dunkeld)
In Wales:
- The Conwy Valley Line at Llanwrst
- Deganwy and Llandudno Station
- The North Wales Coast from Penmaenmawr to Holyhead
- The Borderlands Line at Penyfford and Dee Marsh Junction
- The Welsh Marshes Line between Gobowen North and Little Mill Junction
- The Maesteg Branch at Tondu
- Ferryside on the South Wales Main Line
I do appologise for the long post but I do hope that you find it somewhat informative!