Both path (mod stock engine or convert engine) have pros & cons. U have to really think about it before deciding which path to choose.
There're several questions u gotta ask urself 1st :
1. How much power do u want before u can settle down & feel satisfied? 0-100kmh in 10 seconds? 8 seconds? 6 seconds?
2. How do want to spend ur money? Do u want to mod step by step, or do it in one shot?
3. How much compromise to ur car u can accept? Lower car resale value? More prone to JPJ roadblock? Car is more prone to breakdown? Car feels sluggish for town driving? Car is stripped out like drag car? Change in driving style?
Either path, leaving ur car in workshop for some time will be (almost) unavoidable. If convert engine, sure u won't be able to use ur car for a while, but even if u choose to mod stock engine, when the mod becomes more & more extensive, sooner or later u also have to start leaving ur car in workshop.
Make ur decision wisely. Modding engine to the max is a long journey :)