Just a couple of questions, comments and suggestions.
Questions
What is the STSS Pro? Are you referring to one of the HD tuners, i.e., SESPT or the SEPST? or something else.
What is the year and model of the bike?
How many miles on the bike?
I do not see the cost of boring cylinders or the cost of new pistons.
I do not see the cost of a dyno tune as dbmg has pointed out.
Have you already upgraded to Stage I? What air filter and exhaust?
Comments
Depending on the model year and mileage, you may not need to replace the lifters.
Unless warranty is an issue, HD cams can be replace with better aftermarket cams but if warranty is an issue, the SE 204, IMHO, would be a better choice than the SE259. If not having heads ported, the stock heads are not capable of taking advantage of the higher lift cams. The SE204 cams will also produce a better TQ curve than the 259 which are not bad cams but need more than stock compression to shine.
Perfect fit pushrods are not required if the cams selected are lower lift cams like the SE204 with lifts in the .510" range; stock pushrods will work.
In either configuration, 96" or 103", SE valve springs are not required; the OEM beehive springs will work fine in this mild upgrade.
Suggestions
Not knowing what your performance goals are makes it hard to give informed advice but if 90/90 numbers are your goal and $3100 is within your budget you need to know that you can get real close to 90/90 for much less. To simplify the related cost, the costs I refer to will be in USD; 3086CAD = $2340USD; $1286 in parts and $1054USD in labor.
A cam only upgrade, fuel management system and dyno tune can get you in the 85HP/100TQ neighborhood for about $1250USD in parts (cams, tuner and dyno tune) plus $625UD for 8 labor hours $78USD/hour for total cost of $1875USD/2475CAD. If you should need lifters and pushrods, add $300USD to that total. Note that both figures exceed your current projected cost of $2340USD because I believe you have missed some items in your above listed cost projections.
Now, if you want to go to 103" you should consider changing your plan and looking for numbers in the 100HP/110 range but, of course, that means "mo money".
A strong 103" configuration will cost somewhere in the neighborhood of $1850USD/2442CAD plus your projected labor cost of $1054USD/1390CAD for a total cost of $2904USD/3832CAD. This would include boring cylinders, fitting new pistons, cams, pushrods, lifters, gaskets, tuner and dyno tune. With the right cam and tune, this configuration can produce 100HP/110TQ numbers easy. Add headwork at a cost of another $500USD and those numbers go up even more.
Now, I throw the curve. The new 110" drop in piston cylinder kit from HD cost about $1100USD from an online discount dealer. Unfortunately, dealers in the lower 48 will not ship to "foreign" countries, so you would have to have someone down south purchase and mail, or pay retail at a local HD dealer. Substituting the 110" kit for the 103" pistons and cylinders will add about $800 to the price to go to 103" but you are then looking at 110+HP/125+TQ.
It's all about what your performance goals are and how much you can afford to achieve those goals. You have to pay to play.