Considering a engine upgrade
Bike had 33k on it at the time.
I, like you, had a 96 with Andrews 48s and was clocking about 98 ft lbs of torque. I was tuned with the fp3 and ran V&H true duals with cobra 3.5 slip ons.
Bike ran solid got great fuel economy and sounded good but at the end of the summer before I upgraded started to get hot and was down on power.
I scheduled my appointment with FM, drove up one afternoon before the scheduled day and dropped the bike off right after they opened.
FM completed my bike that afternoon and called saying I could pick up the next day.
I did 107, level b heads, woods 777 cams and FM air cleaner.
Had purchased a PV before the upgrade dumping the FP3.
I ended up right at 123 ft lbs of torque and around 115 hp.
Bike runs great, fuel economy is Rock solid, engine no longer gets hot and I have power in any gear across the power range.
All total I'm in, including the PV around $4K.
I'd do it again, in a heartbeat.
PS, I still have original comp, and have ridden over 10k this summer after the upgrade and the only service issue I have had is a failed front fork seal.
My experience, yours could vary.
As for true dual exhausts, that is how most twins came in the past. Then during the '60s IIRC BSA discovered by chance that adding a balance pipe between the separate exhausts improved low/mid range performance significantly, over separate pipes. That is why today every twin-cylinder bike made comes stock with some sort of siamesed system, including our Harleys. So to get the best out of your upgrade, go with the flow!
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I upgraded from a 96" with a 48h cam as well.
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