Hi Mr. Tuggles,
I had the exact same problem this week. Last week I replaced a bunch of things on my 9800- lcd, digitizer, main flex cable, trackpad, and slide mechanism. The new lcd made all the colors much more rich and it really seemed like a brand new phone. Applications opened much more quickly and the scrolling was less laggy. I was very pleased.
A few days later my trackpad won't click. I move the trackpad around and move the menu over from 'all' to 'favorites'. Pressing call-end button doesn't return it to the 'all' tab. So I start trying every button and my send, end, and trackpad click doesn't work. I'm like f**k. I recently replaced sealed the digitizer to the lcd thinking it was gonna be a permanent fix and now i'm gonna have to do it all over again just to remove the slide mechanism. I thought to myself: before I mess up all the hard work I'll just fiddle with the trackpad and call/end/back/menu key conector.
So I took the phone apart only up to the point where you take the front half off and unscrew the little bracket covering the trackpad connector and call/menu/back/end keys connector. I disconnected the trackpad and slowly firmly reconnected it. I disconnected the call/menu/back/end connecter to the main flex, blew on both ends, and firmly reconnected it.
Then I remembered something very important! When I replaced the main flex cable a few days previous it seemed a touch too long for the slide mechanism. I had to sort of tuck it the top part when screwing the slide mechanism to the front part and tuck it in at the bottom where that plastic bracket covers the connectors to the trackpad etc. There is even a little nipple-like tab and a hole in the flex cable just below where the trackpad connecter is. They weren't meeting up. My rationale is that the too long main flex cable when tucked in bends a bit. This puts force on the connector and with enough trackpad clicking and button pressing it slightly comes apart. This slight coming apart causes the above mentioned symptoms. So after reconnecting the trackpad and keys I wiggled the flex cable where the trackpad connects enough that the tab fit in the hole and I was able to get the plastic bracket over that and screw it in. I assembled the phone. Now the 5 minute waiting period where it freaking boots up...
Success! It works for now. Who knows maybe in a couple weeks I'll do the dance again but for now it's back to being snappy. This was one thing I didn't need. The 9800 has so much bulls**t that comes with it (no tmobile service books, white screen of death, reboot loops, constant OS reinstallations) that I didn't need this. I feel for you if this problem you have is almost the last straw.
I don't know if you at all have ever taken your phone apart or you pay people to do it but I included what I did if you ever wanted to do it urself. If not show your phone doctor this boring tale and just highlight the important parts. If it didn't work for me I was going to get another main flex cable and start from there but luckily I didn't have to. All the best and lets hope BB10 phones are as low maintenance as my playbook (which doesn't need a restart after every setting/app change).