I've done a few engine swaps over the years and all of them have presented their own unique problems Jim. I've currently got the Trackmaster Benelli on the jig so I'm also feeling the brain pain my friend
There are a couple of key rules that both make the job easier and more importantly make the finished product a successful operation. Set the bare frame up on a milk crate or a block of some kind. Like Graeme said, try and do the job with a set of empty cases to save your knuckles, lifting the motor in and out. I'd still have the gearbox fitted to enable you to align the sprocket and to help place the pegs in conjunction to the gear lever. First thing though is to fit the back wheel that you intend to use complete with sprocket and all spacers in place. Make sure it's centrally located and nipped up and running true and straight.
When placing the engine don't rush, take it easy as getting the alignment right is the most important pieces of the engine swap puzzle. I use wooden wedges placed under the engine to jiggle it around until you get it in the right place. Try and locate the drive sprocket totally parallel and as close to the swingarm pivot as possible without the engine cases touching the frame or swingarm. Make sure the sprockets run absolutely parallel with each other. I use a builders laser level, running the laser beam from the rear sprocket directly forward towards the front of the bike. Jiggle the engine into place until the both sprockets are totally in line with each other along the line of the laser beam (
if you're not laser equipped, a good strait edge does the same job but it's a bit more awkward) Chock the engine as securely as possibly with wedges and/or different thickness wooden packing pieces, making sure that no part of the engine cases are sitting on or up against any frame tubing. About 7-10mm clearance is what you want.
You're now ready to make your mounts. Assuming the original frame mounts have been removed, I use perspex that's thin enough to cut with scissors to make my mounting templates. Being transparent makes it easier to see what needs trimming or cutting. As Brent says, you may get lucky with some of the mounts being in the right place but don't bank on it. It's a tedious job that is impossible to generalise on. Each swap has it's own unique problems. Some can use welded mounts while others will require alloy engine plates that enable the engine to be removed sideways or with the plates intact. When you think you've got it right, just tack the mounts in until you're sure the engine can be removed and refitted without having to cut the mounts out. You'll need to dummy fit the barrel and head to make sure there's enough top rail clearance for engine removal.
I once bought an abandoned project Honda XL350 powered CZ which upon initial inspection looked to be a very neat conversion. Unfortunately, the original builder hadn't factored in the eventual removal of the engine and had welded the mounts in place with the rocker cover 5 mm from the top frame rail and the mounts welded in place so the engine couldn't be removed sideways. I had to oxy cut the engine mounts out to remove the engine. To fix the problem took some major re engineering that I won't go into here but it was a
big job. I almost did a similar fu*k up myself when I fitted the Triumph 500 engine to my Bultaco M11 Metisse. Great little swap alright but with the rocker covers almost touching the top rail, I couldn't remove the motor by lifting it up and out. I got around it by using alloy plates which could be removed, enabling the engine to be removed sideways.
What are you actually building Jim? If you like maybe I can come over one day and give you a hand setting it up. That's easier than trying to describe a process without actually seeing the unique situation in front of us. Engine swaps aren't a walk in the park, some are pretty straight forward ' just reweld in another place' mount changes while others require major frame redesign. This Tracky/Benelli I'm now into is a bit of both.
